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CHECK report for mzR on tokay1

This page was generated on 2021-05-06 12:32:25 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the mzR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1195/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mzR 2.24.1  (landing page)
Steffen Neumann
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/mzR
Branch: RELEASE_3_12
Last Commit: e1d4de8
Last Changed Date: 2020-11-18 08:39:00 -0400 (Wed, 18 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: mzR
Version: 2.24.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mzR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings mzR_2.24.1.tar.gz
StartedAt: 2021-05-06 04:59:38 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:06:25 -0400 (Thu, 06 May 2021)
EllapsedTime: 407.2 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: mzR.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mzR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings mzR_2.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/mzR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mzR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mzR' version '2.24.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'mzR' can be installed ... WARNING
Found the following significant warnings:
  cramp.h:261:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampScanInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  cramp.h:315:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampRunInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  cramp.h:149:10: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder]
  cramp.h:148:18: warning:   'rampRunInfo* cRamp::m_runInfo' [-Wreorder]
  cramp.cpp:72:1: warning:   when initialized here [-Wreorder]
  ramp.cpp:2799:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation]
  ramp.cpp:2812:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation]
  ramp.cpp:2816:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation]
  ./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  ./boost/boost/iostreams/chain.hpp:256:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  RcppPwiz.cpp:745:29: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=]
  pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation]
  pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: 'pwiz::identdata::{anonymous}::Handler_protXML::strict' will be initialized after [-Wreorder]
  pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning:   'int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides' [-Wreorder]
  pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning:   when initialized here [-Wreorder]
  pwiz/data/proteome/Modification.cpp:89:5: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  pwiz/utility/minimxml/SAXParser.cpp:431:20: warning: offset '1' outside bounds of constant string [-Warray-bounds]
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/mzR.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for 'Rhdf5lib' is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
  -fpermissive
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/mzR/libs/i386/mzR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/mzR/libs/x64/mzR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/mzR.Rcheck/00check.log'
for details.

Installation output

mzR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/mzR_2.24.1.tar.gz && rm -rf mzR.buildbin-libdir && mkdir mzR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mzR.buildbin-libdir mzR_2.24.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL mzR_2.24.1.zip && rm mzR_2.24.1.tar.gz mzR_2.24.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4777k  100 4777k    0     0  70.7M      0 --:--:-- --:--:-- --:--:-- 71.7M

install for i386

* installing *source* package 'mzR' ...
** using staged installation
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./pwiz/data/msdata/ramp/wglob.o ./boost_aux/boost/nowide/iostream.o rampR.o 
find . -name \*~ -exec rm {} \;   ## from cleanup
find . -name \*.o -exec rm {} \;  ## from cleanup
find . -name "#*#" -exec rm {} \; ## from cleanup
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cramp.cpp -o cramp.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from random_access_gzFile.h:21,
                 from ramp.h:72,
                 from cramp.h:33,
                 from cramp.cpp:49:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from cramp.cpp:49:
cramp.h: In copy constructor 'rampScanInfo::rampScanInfo(rampScanInfo&)':
cramp.h:261:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampScanInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
         memmove(this,&rhs,sizeof(rhs));
                                      ^
In file included from cramp.cpp:49:
cramp.h:251:7: note: 'class rampScanInfo' declared here
 class rampScanInfo: public rampInfo
       ^~~~~~~~~~~~
In file included from cramp.cpp:49:
cramp.h: In copy constructor 'rampRunInfo::rampRunInfo(const rampRunInfo&)':
cramp.h:315:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampRunInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
         memmove(this,&rhs,sizeof(rhs));
                                      ^
cramp.h:305:7: note: 'class rampRunInfo' declared here
 class rampRunInfo: public rampInfo
       ^~~~~~~~~~~
In file included from cramp.cpp:49:
cramp.h: In constructor 'cRamp::cRamp(const char*, bool)':
cramp.h:149:10: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder]
     bool m_declaredScansOnly; // if true, suppress RAMP's habit of adding scans to fill in between declared scans
          ^~~~~~~~~~~~~~~~~~~
cramp.h:148:18: warning:   'rampRunInfo* cRamp::m_runInfo' [-Wreorder]
     rampRunInfo *m_runInfo; // scan count etc
                  ^~~~~~~~~
cramp.cpp:72:1: warning:   when initialized here [-Wreorder]
 cRamp::cRamp( const char* fileName,bool declaredScansOnly ) :
 ^~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ramp_base64.cpp -o ramp_base64.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ramp.cpp -o ramp.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from random_access_gzFile.h:21,
                 from ramp.h:72,
                 from ramp.cpp:44:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
ramp.cpp:248:23: warning: unused variable 'fgot' [-Wunused-variable]
                 char *fgot=ramp_fgets(buf,sizeof(buf)-1,result);
                       ^~~~
ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
ramp.cpp:451:12: warning: unused variable 'nread' [-Wunused-variable]
     size_t nread = ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI);
            ^~~~~
ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
ramp.cpp:650:31: warning: unused variable 'fgot' [-Wunused-variable]
                         char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                               ^~~~
ramp.cpp:692:31: warning: unused variable 'fgot' [-Wunused-variable]
                         char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                               ^~~~
ramp.cpp:729:27: warning: unused variable 'fgot' [-Wunused-variable]
                     char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                           ^~~~
ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
ramp.cpp:1446:27: warning: unused variable 'fgot' [-Wunused-variable]
                     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                           ^~~~
ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:1532:15: warning: unused variable 'fgot' [-Wunused-variable]
         char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
               ^~~~
ramp.cpp:1528:11: warning: unused variable 'fgot' [-Wunused-variable]
     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
           ^~~~
ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:2090:28: warning: unused variable 'nread' [-Wunused-variable]
                     size_t nread = ramp_fread(pData+partial,(int)(peaksLen-partial), pFI);
                            ^~~~~
ramp.cpp:2293:27: warning: unused variable 'fgot' [-Wunused-variable]
                     char *fgot=ramp_fgets(buf, sizeof(buf)-1 , pFI);
                           ^~~~
ramp.cpp:2340:24: warning: unused variable 'nread' [-Wunused-variable]
                 size_t nread = ramp_fread(pData+partial,peaksLen-partial, pFI);
                        ^~~~~
ramp.cpp:2394:21: warning: variable 'err' set but not used [-Wunused-but-set-variable]
                 int err;
                     ^~~
ramp.cpp:2212:19: warning: unused variable 'fgot' [-Wunused-variable]
             char *fgot=ramp_fgets(buf, sizeof(buf)-1, pFI);
                   ^~~~
ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
ramp.cpp:2520:15: warning: unused variable 'fgot' [-Wunused-variable]
         char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
               ^~~~
ramp.cpp:2544:15: warning: unused variable 'fgot' [-Wunused-variable]
         char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
               ^~~~
ramp.cpp:2516:11: warning: unused variable 'fgot' [-Wunused-variable]
     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
           ^~~~
ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
ramp.cpp:2695:19: warning: unused variable 'fgot' [-Wunused-variable]
             char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                   ^~~~
ramp.cpp:2731:19: warning: unused variable 'fgot' [-Wunused-variable]
             char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                   ^~~~
ramp.cpp:2682:11: warning: unused variable 'fgot' [-Wunused-variable]
     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
           ^~~~
ramp.cpp: In function 'int rampSelfTest(char*)':
ramp.cpp:2799:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation]
         strncpy(buf,testname[i],sizeof(buf));
         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ramp.cpp:2812:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation]
         strncpy(buf,filename,sizeof(buf));
         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
ramp.cpp:2816:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation]
         strncpy(buf,filename,sizeof(buf));
         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppRamp.cpp -o RcppRamp.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from random_access_gzFile.h:21,
                 from ramp.h:72,
                 from cramp.h:33,
                 from RcppRamp.h:14,
                 from RcppRamp.cpp:1:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from RcppRamp.h:14,
                 from RcppRamp.cpp:1:
cramp.h: In copy constructor 'rampScanInfo::rampScanInfo(rampScanInfo&)':
cramp.h:261:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampScanInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
         memmove(this,&rhs,sizeof(rhs));
                                      ^
In file included from RcppRamp.h:14,
                 from RcppRamp.cpp:1:
cramp.h:251:7: note: 'class rampScanInfo' declared here
 class rampScanInfo: public rampInfo
       ^~~~~~~~~~~~
In file included from RcppRamp.h:14,
                 from RcppRamp.cpp:1:
cramp.h: In copy constructor 'rampRunInfo::rampRunInfo(const rampRunInfo&)':
cramp.h:315:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampRunInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
         memmove(this,&rhs,sizeof(rhs));
                                      ^
cramp.h:305:7: note: 'class rampRunInfo' declared here
 class rampRunInfo: public rampInfo
       ^~~~~~~~~~~
RcppRamp.cpp: In member function 'Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo()':
RcppRamp.cpp:215:27: warning: unused variable 'info' [-Wunused-variable]
             rampScanInfo *info = ramp->getScanHeaderInfo( 1 );
                           ^~~~
RcppRamp.cpp: In member function 'Rcpp::NumericMatrix RcppRamp::get3DMap(std::vector<int>, double, double, double)':
RcppRamp.cpp:388:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for (int i = 0; i < scanNumbers.size(); i++)
                         ~~^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppRampModule.cpp -o RcppRampModule.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from random_access_gzFile.h:21,
                 from ramp.h:72,
                 from cramp.h:33,
                 from RcppRamp.h:14,
                 from RcppRampModule.cpp:2:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from RcppRamp.h:14,
                 from RcppRampModule.cpp:2:
cramp.h: In copy constructor 'rampScanInfo::rampScanInfo(rampScanInfo&)':
cramp.h:261:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampScanInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
         memmove(this,&rhs,sizeof(rhs));
                                      ^
In file included from RcppRamp.h:14,
                 from RcppRampModule.cpp:2:
cramp.h:251:7: note: 'class rampScanInfo' declared here
 class rampScanInfo: public rampInfo
       ^~~~~~~~~~~~
In file included from RcppRamp.h:14,
                 from RcppRampModule.cpp:2:
cramp.h: In copy constructor 'rampRunInfo::rampRunInfo(const rampRunInfo&)':
cramp.h:315:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampRunInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
         memmove(this,&rhs,sizeof(rhs));
                                      ^
cramp.h:305:7: note: 'class rampRunInfo' declared here
 class rampRunInfo: public rampInfo
       ^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppPwiz.cpp -o RcppPwiz.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from RcppPwiz.h:12,
                 from RcppPwiz.cpp:1:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Std.hpp:31,
                 from RcppPwiz.h:20,
                 from RcppPwiz.cpp:1:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from pwiz/utility/misc/Std.hpp:32,
                 from RcppPwiz.h:20,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from ./boost/boost/iostreams/filtering_stream.hpp:22,
                 from RcppPwiz.h:23,
                 from RcppPwiz.cpp:1:
./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)':
./boost/boost/iostreams/chain.hpp:256:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getScanHeaderInfo(Rcpp::IntegerVector)':
RcppPwiz.cpp:133:9: warning: unused variable 'N' [-Wunused-variable]
     int N = slp->size();
         ^
RcppPwiz.cpp: In member function 'void RcppPwiz::addSpectrumList(pwiz::msdata::MSData&, Rcpp::DataFrame&, Rcpp::List&, bool)':
RcppPwiz.cpp:745:29: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
     if (precursorScanNum[i] > 0 | precursorMZ[i] > 0) {
RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)':
RcppPwiz.cpp:820:49: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {
                                      ~~~~~~~~~~~^~~~~~~~~~~~~
RcppPwiz.cpp:830:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::msdata::TimeIntensityPair>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for (int i = 0; i < pairs.size(); i++) {
                       ~~^~~~~~~~~~~~~~
RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo(Rcpp::IntegerVector)':
RcppPwiz.cpp:850:10: warning: unused variable 'nativeIdFormat_' [-Wunused-variable]
     CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd);
          ^~~~~~~~~~~~~~~
RcppPwiz.cpp: In member function 'Rcpp::NumericMatrix RcppPwiz::get3DMap(std::vector<int>, double, double, double)':
RcppPwiz.cpp:981:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for (int i = 0; i < scanNumbers.size(); i++)
                       ~~^~~~~~~~~~~~~~~~~~~~
RcppPwiz.cpp:987:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::msdata::MZIntensityPair>::size_type' {aka 'unsigned int'} [-Wsign-compare]
    for (int k=0; k < pairs.size(); k++)
                  ~~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppPwizModule.cpp -o RcppPwizModule.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from RcppPwiz.h:12,
                 from RcppPwizModule.cpp:2:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Std.hpp:31,
                 from RcppPwiz.h:20,
                 from RcppPwizModule.cpp:2:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from pwiz/utility/misc/Std.hpp:32,
                 from RcppPwiz.h:20,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from ./boost/boost/iostreams/filtering_stream.hpp:22,
                 from RcppPwiz.h:23,
                 from RcppPwizModule.cpp:2:
./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)':
./boost/boost/iostreams/chain.hpp:256:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppIdent.cpp -o RcppIdent.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Std.hpp:31,
                 from RcppIdent.h:14,
                 from RcppIdent.cpp:1:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from pwiz/utility/misc/Std.hpp:32,
                 from RcppIdent.h:14,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
RcppIdent.cpp: In member function 'Rcpp::DataFrame RcppIdent::getScore()':
RcppIdent.cpp:293:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    for (size_t j = 0; j < nCvParams; j++) {
                       ~~^~~~~~~~~~~
RcppIdent.cpp: In member function 'Rcpp::List RcppIdent::getPara()':
RcppIdent.cpp:382:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::data::CVParam>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 0 ; i < sip[0]->additionalSearchParams.cvParams.size(); i++)
                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RcppIdent.cpp:388:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::data::UserParam>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++)
                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppIdentModule.cpp -o RcppIdentModule.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Std.hpp:31,
                 from RcppIdent.h:14,
                 from RcppIdentModule.cpp:2:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from pwiz/utility/misc/Std.hpp:32,
                 from RcppIdent.h:14,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/system/config.hpp:13,
                 from ./boost/boost/system/error_code.hpp:14,
                 from boost/libs/system/src/error_code.cpp:16:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/posix_api.cpp:21:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/fileiter.cpp -o boost/libs/regex/src/fileiter.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/fileiter.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex_raw_buffer.cpp -o boost/libs/regex/src/regex_raw_buffer.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/regex_raw_buffer.cpp:21:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/cregex.cpp -o boost/libs/regex/src/cregex.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from ./boost/boost/regex.hpp:28,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/regex_debug.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/instances.cpp -o boost/libs/regex/src/instances.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/instances.cpp:21:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/icu.cpp -o boost/libs/regex/src/icu.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/icu.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/usinstances.cpp -o boost/libs/regex/src/usinstances.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/detail/workaround.hpp:41,
                 from boost/libs/regex/src/usinstances.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/regex.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/wide_posix_api.cpp:21:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex_traits_defaults.cpp -o boost/libs/regex/src/regex_traits_defaults.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from ./boost/boost/regex/regex_traits.hpp:23,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/winstances.cpp -o boost/libs/regex/src/winstances.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/winstances.cpp:21:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/wc_regex_traits.cpp -o boost/libs/regex/src/wc_regex_traits.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/detail/workaround.hpp:41,
                 from boost/libs/regex/src/wc_regex_traits.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/c_regex_traits.cpp -o boost/libs/regex/src/c_regex_traits.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/c_regex_traits.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/cpp_regex_traits.cpp -o boost/libs/regex/src/cpp_regex_traits.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/static_mutex.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/w32_regex_traits.cpp -o boost/libs/regex/src/w32_regex_traits.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/w32_regex_traits.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/range/iterator_range.hpp:13,
                 from ./boost/boost/iostreams/traits.hpp:39,
                 from ./boost/boost/iostreams/detail/dispatch.hpp:17,
                 from ./boost/boost/iostreams/read.hpp:19,
                 from ./boost/boost/iostreams/detail/buffer.hpp:20,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:49,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/iostreams/src/file_descriptor.cpp:16:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/filesystem/operations.hpp:18,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/filesystem/path.hpp:28,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/filesystem/src/path.cpp:12:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/filesystem/path.hpp:28,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/utf8_codecvt_facet.cpp:15:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/chrono/config.hpp:15,
                 from ./boost/boost/chrono/duration.hpp:33,
                 from ./boost/boost/chrono/chrono.hpp:11,
                 from ./boost/boost/chrono/detail/inlined/chrono.hpp:13,
                 from boost/libs/chrono/src/chrono.cpp:14:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/chrono/config.hpp:15,
                 from ./boost/boost/chrono/detail/inlined/process_cpu_clocks.hpp:15,
                 from boost/libs/chrono/src/process_cpu_clocks.cpp:17:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/chrono/config.hpp:15,
                 from ./boost/boost/chrono/detail/inlined/thread_clock.hpp:14,
                 from boost/libs/chrono/src/thread_clock.cpp:18:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/MemoryIndex.cpp:26:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/MemoryIndex.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/common/MemoryIndex.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/checked_delete.hpp:15,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:26,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::MemoryIndex::Impl]':
./boost/boost/smart_ptr/detail/shared_count.hpp:134:34:   required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::MemoryIndex::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:271:20:   required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::data::MemoryIndex::Impl; Y = pwiz::data::MemoryIndex::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:349:44:   required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::data::MemoryIndex::Impl; T = pwiz::data::MemoryIndex::Impl]'
pwiz/data/common/MemoryIndex.cpp:73:58:   required from here
./boost/boost/core/checked_delete.hpp:34:5: warning: deleting object of polymorphic class type 'pwiz::data::MemoryIndex::Impl' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete x;
     ^~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/range/iterator_range.hpp:13,
                 from ./boost/boost/range/as_literal.hpp:22,
                 from ./boost/boost/algorithm/string/predicate.hpp:19,
                 from pwiz/data/common/CVTranslator.cpp:28:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:29:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/common/CVTranslator.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)':
pwiz/data/common/CVTranslator.cpp:133:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:135:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:136:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from pwiz/data/common/cv.cpp:24765:
pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)':
pwiz/data/common/cv.inl:102:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
         for (int o=0;o<oboPrefixesSize_;++o)
                      ~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/ParamTypes.cpp:28:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/common/ParamTypes.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/spirit/home/karma/string.hpp:13,
                 from ./boost/boost/spirit/home/karma.hpp:14,
                 from ./boost/boost/spirit/include/karma.hpp:16,
                 from pwiz/data/common/ParamTypes.cpp:29:
./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string<String, CharEncoding, Tag, no_attribute>::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const':
./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs]
                 extracted_string_type;
                 ^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.cpp:26:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/BinaryIndexStream.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/common/BinaryIndexStream.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
In file included from ./boost/boost/checked_delete.hpp:15,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:26,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::BinaryIndexStream::Impl]':
./boost/boost/smart_ptr/detail/shared_count.hpp:134:34:   required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:271:20:   required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::data::BinaryIndexStream::Impl; Y = pwiz::data::BinaryIndexStream::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:349:44:   required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl; T = pwiz::data::BinaryIndexStream::Impl]'
pwiz/data/common/BinaryIndexStream.cpp:402:103:   required from here
./boost/boost/core/checked_delete.hpp:34:5: warning: deleting object of polymorphic class type 'pwiz::data::BinaryIndexStream::Impl' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete x;
     ^~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from pwiz/data/common/diff_std.cpp:27:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost_aux/boost/enum/iterator.hpp:18,
                 from ./boost_aux/boost/enum.hpp:18,
                 from pwiz/data/common/Unimod.hpp:31,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost_aux/boost/enum/bitfield.hpp:22,
                 from ./boost_aux/boost/enum.hpp:20,
                 from pwiz/data/common/Unimod.hpp:31,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/common/Unimod.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/function/detail/maybe_include.hpp:23,
                 from ./boost/boost/function/detail/function_iterate.hpp:14,
                 from ./boost/boost/preprocessor/iteration/detail/iter/forward1.hpp:57,
                 from ./boost/boost/function.hpp:64,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost_aux/boost/enum/bitfield.hpp:22,
                 from ./boost_aux/boost/enum.hpp:20,
                 from pwiz/data/common/Unimod.hpp:31,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/function/function_template.hpp: In instantiation of 'void boost::detail::function::basic_vtable2<R, T0, T1>::assign_functor(FunctionObj, boost::detail::function::function_buffer&, mpl_::true_) const [with FunctionObj = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; mpl_::true_ = mpl_::bool_<true>]':
./boost/boost/function/function_template.hpp:608:13:   required from 'bool boost::detail::function::basic_vtable2<R, T0, T1>::assign_to(FunctionObj, boost::detail::function::function_buffer&, boost::detail::function::function_obj_tag) const [with FunctionObj = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:498:45:   required from 'bool boost::detail::function::basic_vtable2<R, T0, T1>::assign_to(F, boost::detail::function::function_buffer&) const [with F = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:942:7:   required from 'void boost::function2<R, T1, T2>::assign_to(Functor) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:728:7:   required from 'boost::function2<R, T1, T2>::function2(Functor, typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type = int]'
./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36:   required from 'boost::algorithm::detail::find_iterator_base<IteratorT>::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/find_iterator.hpp:265:29:   required from 'boost::algorithm::split_iterator<IteratorT>::split_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/iter_find.hpp:170:21:   required from 'SequenceSequenceT& boost::algorithm::iter_split(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector<std::__cxx11::basic_string<char> >; RangeT = const std::__cxx11::basic_string<char>; FinderT = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>]'
./boost/boost/algorithm/string/split.hpp:146:50:   required from 'SequenceSequenceT& boost::algorithm::split(SequenceSequenceT&, RangeT&, PredicateT, boost::algorithm::token_compress_mode_type) [with SequenceSequenceT = std::vector<std::__cxx11::basic_string<char> >; RangeT = const std::__cxx11::basic_string<char>; PredicateT = boost::algorithm::detail::is_classifiedF]'
pwiz/data/common/Unimod.cpp:129:71:   required from here
./boost/boost/function/function_template.hpp:572:49: warning: placement new constructing an object of type 'boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>' and size '12' in a region of type 'char' and size '1' [-Wplacement-new=]
           new (reinterpret_cast<void*>(&functor.data)) FunctionObj(f);
                                         ~~~~~~~~^~~~
In file included from ./boost/boost/function/detail/prologue.hpp:17,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost_aux/boost/enum/bitfield.hpp:22,
                 from ./boost_aux/boost/enum.hpp:20,
                 from pwiz/data/common/Unimod.hpp:31,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/function/function_base.hpp: In instantiation of 'static void boost::detail::function::functor_manager_common<Functor>::manage_small(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>]':
./boost/boost/function/function_base.hpp:364:56:   required from 'static void boost::detail::function::functor_manager<Functor>::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, mpl_::true_) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; mpl_::true_ = mpl_::bool_<true>]'
./boost/boost/function/function_base.hpp:412:18:   required from 'static void boost::detail::function::functor_manager<Functor>::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, boost::detail::function::function_obj_tag) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>]'
./boost/boost/function/function_base.hpp:440:20:   required from 'static void boost::detail::function::functor_manager<Functor>::manage(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>]'
./boost/boost/function/function_template.hpp:940:13:   required from 'void boost::function2<R, T1, T2>::assign_to(Functor) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:728:7:   required from 'boost::function2<R, T1, T2>::function2(Functor, typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type = int]'
./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36:   required from 'boost::algorithm::detail::find_iterator_base<IteratorT>::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/find_iterator.hpp:265:29:   required from 'boost::algorithm::split_iterator<IteratorT>::split_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/iter_find.hpp:170:21:   required from 'SequenceSequenceT& boost::algorithm::iter_split(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector<std::__cxx11::basic_string<char> >; RangeT = const std::__cxx11::basic_string<char>; FinderT = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>]'
./boost/boost/algorithm/string/split.hpp:146:50:   required from 'SequenceSequenceT& boost::algorithm::split(SequenceSequenceT&, RangeT&, PredicateT, boost::algorithm::token_compress_mode_type) [with SequenceSequenceT = std::vector<std::__cxx11::basic_string<char> >; RangeT = const std::__cxx11::basic_string<char>; PredicateT = boost::algorithm::detail::is_classifiedF]'
pwiz/data/common/Unimod.cpp:129:71:   required from here
./boost/boost/function/function_base.hpp:318:54: warning: placement new constructing an object of type 'boost::detail::function::functor_manager_common<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF> >::functor_type' {aka 'boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>'} and size '12' in a region of type 'char' and size '1' [-Wplacement-new=]
             new (reinterpret_cast<void*>(&out_buffer.data)) functor_type(*in_functor);
                                           ~~~~~~~~~~~^~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/smart_ptr.hpp:19,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/smart_ptr.hpp:19,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/smart_ptr.hpp:19,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/smart_ptr.hpp:19,
                 from ./pwiz/data/msdata/SpectrumWorkerThreads.hpp:27,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:28:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:29:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:29:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:31:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/examples.cpp:26:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/examples.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mzML.cpp:33:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Serializer_mzML.cpp:33:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.cpp:28:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Serializer_MSn.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/msdata/Reader.cpp:27:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Reader.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.cpp:27:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Serializer_MGF.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/spirit/home/karma/string.hpp:13,
                 from ./boost/boost/spirit/home/karma.hpp:14,
                 from ./boost/boost/spirit/include/karma.hpp:16,
                 from pwiz/data/msdata/Serializer_MGF.cpp:29:
./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string<String, CharEncoding, Tag, no_attribute>::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const':
./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs]
                 extracted_string_type;
                 ^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:33:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:34:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:30:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:30:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:32:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:32:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:28:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:31:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:31:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:29:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:29:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/range/iterator_range.hpp:13,
                 from ./boost/boost/iostreams/traits.hpp:39,
                 from ./boost/boost/iostreams/pipeline.hpp:18,
                 from ./boost/boost/iostreams/detail/push.hpp:22,
                 from ./boost/boost/iostreams/chain.hpp:29,
                 from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:30:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:30:
./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)':
./boost/boost/iostreams/chain.hpp:256:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/iostreams/copy.hpp:26,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:32:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:38:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::__cxx11::string&, size_t*)':
pwiz/data/msdata/BinaryDataEncoder.cpp:280:37: warning: 'byteCount' may be used uninitialized in this function [-Wmaybe-uninitialized]
         filterArray<zlib_compressor>(byteBuffer, byteCount,compressed);
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/BinaryDataEncoder.cpp:280:37: warning: 'byteBuffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Diff.cpp:28:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Diff.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/MSData.cpp:26:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/MSData.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/References.cpp:26:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/References.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:29:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:30:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/msdata/SpectrumList_mzXML.cpp: In constructor 'pwiz::msdata::{anonymous}::SpectrumList_mzXMLImpl::SpectrumList_mzXMLImpl(boost::shared_ptr<std::basic_istream<char> >, const pwiz::msdata::MSData&, bool)':
pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=]
     } catch (index_not_found e){
                              ^
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:30:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/SpectrumList_mzXML.cpp:730:46: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized]
         spectrumIdentity->sourceFilePosition = lexical_cast<stream_offset>(text);
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/SpectrumList_mzXML.cpp:683:22: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized]
         indexOffset_ = lexical_cast<stream_offset>(text);
         ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/msdata/IO.cpp:29:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/IO.cpp:30:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerBinaryDataArray::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:1727:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
                 if (!dataProcessingRef.empty())
                 ^~
pwiz/data/msdata/IO.cpp:1730:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
                     getAttribute(attributes, "encodedLength", encodedLength_, NoXMLUnescape);
                     ^~~~~~~~~~~~
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2020:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList")
                      ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2731:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
         else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
                  ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:29:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:30:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:30:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumInfo.cpp:29:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumInfo.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:27:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/RAMPAdapter.cpp:31:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/RAMPAdapter.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)',
    inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:283:25:
pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation]
     strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH);
     ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)',
    inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:284:25:
pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation]
     strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH);
     ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)',
    inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:285:25:
pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation]
     strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH);
     ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)',
    inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:286:25:
pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation]
     strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH);
     ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/LegacyAdapter.cpp:31:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/LegacyAdapter.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumIterator.cpp:29:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumIterator.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::equal(const pwiz::msdata::SpectrumIterator::Impl&) const':
pwiz/data/msdata/SpectrumIterator.cpp:125:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return (done() && &that.spectrumList_==&pastEndMarker_ ||
             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_);
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::done() const':
pwiz/data/msdata/SpectrumIterator.cpp:141:34: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
            ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:36:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/MSDataFile.cpp:37:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from ./boost/boost/iostreams/filtering_stream.hpp:22,
                 from pwiz/data/msdata/MSDataFile.cpp:41:
./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)':
./boost/boost/iostreams/chain.hpp:256:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)':
pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
     } else if (init == mask) {
                ~~~~~^~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/multi_index/sequenced_index.hpp:49,
                 from ./pwiz/utility/misc/mru_list.hpp:30,
                 from pwiz/data/msdata/MemoryMRUCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.hpp:28,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumListCache.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Index_mzML.cpp:25:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Index_mzML.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:28:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:28:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:30:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/IdentDataFile.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from ./boost/boost/iostreams/filtering_stream.hpp:22,
                 from pwiz/data/identdata/IdentDataFile.cpp:34:
./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)':
./boost/boost/iostreams/chain.hpp:256:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/identdata/Reader.cpp:27:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/Reader.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/Serializer_protXML.cpp:31:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/Serializer_protXML.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/identdata/Serializer_protXML.cpp: In constructor 'pwiz::identdata::{anonymous}::Handler_protXML::Handler_protXML(pwiz::identdata::IdentData&, const pwiz::util::IterationListenerRegistry*, bool, std::vector<std::__cxx11::basic_string<char> >*)':
pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: 'pwiz::identdata::{anonymous}::Handler_protXML::strict' will be initialized after [-Wreorder]
     bool strict;
          ^~~~~~
pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning:   'int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides' [-Wreorder]
     int nPeptides;
         ^~~~~~~~~
pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning:   when initialized here [-Wreorder]
     Handler_protXML(IdentData& mzid,
     ^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:28:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/identdata/Serializer_pepXML.cpp: In function 'void pwiz::identdata::{anonymous}::write_spectrum_queries(pwiz::minimxml::XMLWriter&, const pwiz::identdata::IdentData&, const string&, const pwiz::util::IterationListenerRegistry*)':
pwiz/data/identdata/Serializer_pepXML.cpp:800:52: warning: 'lastSpectrumIndex' may be used uninitialized in this function [-Wmaybe-uninitialized]
             if (sii.chargeState != lastChargeState || spectrumIndex != lastSpectrumIndex)
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/Serializer_mzid.cpp:30:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/Serializer_mzid.cpp:30:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/identdata/IO.cpp:30:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/IO.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/References.cpp:27:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/References.cpp:27:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/identdata/References.cpp: In function 'void pwiz::identdata::References::resolve(std::vector<boost::shared_ptr<pwiz::identdata::Contact> >&, pwiz::identdata::IdentData&)':
pwiz/data/identdata/References.cpp:148:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
         else if (dynamic_cast<Person*>(c.get()))
                 ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/proteome/Modification.cpp:30:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/proteome/Modification.cpp:30:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/proteome/Modification.cpp:30:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/proteome/Modification.cpp:89:5: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     auto_ptr<Formula> formula_;
     ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/proteome/Digestion.cpp:32:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:32:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/proteome/Digestion.cpp:32:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/function/detail/maybe_include.hpp:23,
                 from ./boost/boost/function/detail/function_iterate.hpp:14,
                 from ./boost/boost/preprocessor/iteration/detail/iter/forward1.hpp:57,
                 from ./boost/boost/function.hpp:64,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:32:
./boost/boost/function/function_template.hpp: In instantiation of 'void boost::detail::function::basic_vtable2<R, T0, T1>::assign_functor(FunctionObj, boost::detail::function::function_buffer&, mpl_::true_) const [with FunctionObj = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; mpl_::true_ = mpl_::bool_<true>]':
./boost/boost/function/function_template.hpp:608:13:   required from 'bool boost::detail::function::basic_vtable2<R, T0, T1>::assign_to(FunctionObj, boost::detail::function::function_buffer&, boost::detail::function::function_obj_tag) const [with FunctionObj = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:498:45:   required from 'bool boost::detail::function::basic_vtable2<R, T0, T1>::assign_to(F, boost::detail::function::function_buffer&) const [with F = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:942:7:   required from 'void boost::function2<R, T1, T2>::assign_to(Functor) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:728:7:   required from 'boost::function2<R, T1, T2>::function2(Functor, typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type = int]'
./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36:   required from 'boost::algorithm::detail::find_iterator_base<IteratorT>::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/find_iterator.hpp:100:26:   required from 'boost::algorithm::find_iterator<IteratorT>::find_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/iter_find.hpp:100:21:   required from 'SequenceSequenceT& boost::algorithm::iter_find(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector<boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > > >; RangeT = const std::__cxx11::basic_string<char>; FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>]'
./boost/boost/algorithm/string/split.hpp:67:49:   required from 'SequenceSequenceT& boost::algorithm::find_all(SequenceSequenceT&, Range1T&, const Range2T&) [with SequenceSequenceT = std::vector<boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > > >; Range1T = const std::__cxx11::basic_string<char>; Range2T = std::__cxx11::basic_string<char>]'
pwiz/data/proteome/Digestion.cpp:472:63:   required from here
./boost/boost/function/function_template.hpp:572:49: warning: placement new constructing an object of type 'boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>' and size '12' in a region of type 'char' and size '1' [-Wplacement-new=]
           new (reinterpret_cast<void*>(&functor.data)) FunctionObj(f);
                                         ~~~~~~~~^~~~
In file included from ./boost/boost/function/detail/prologue.hpp:17,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:32:
./boost/boost/function/function_base.hpp: In instantiation of 'static void boost::detail::function::functor_manager_common<Functor>::manage_small(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>]':
./boost/boost/function/function_base.hpp:364:56:   required from 'static void boost::detail::function::functor_manager<Functor>::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, mpl_::true_) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; mpl_::true_ = mpl_::bool_<true>]'
./boost/boost/function/function_base.hpp:412:18:   required from 'static void boost::detail::function::functor_manager<Functor>::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, boost::detail::function::function_obj_tag) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>]'
./boost/boost/function/function_base.hpp:440:20:   required from 'static void boost::detail::function::functor_manager<Functor>::manage(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>]'
./boost/boost/function/function_template.hpp:940:13:   required from 'void boost::function2<R, T1, T2>::assign_to(Functor) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:728:7:   required from 'boost::function2<R, T1, T2>::function2(Functor, typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type = int]'
./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36:   required from 'boost::algorithm::detail::find_iterator_base<IteratorT>::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/find_iterator.hpp:100:26:   required from 'boost::algorithm::find_iterator<IteratorT>::find_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/iter_find.hpp:100:21:   required from 'SequenceSequenceT& boost::algorithm::iter_find(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector<boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > > >; RangeT = const std::__cxx11::basic_string<char>; FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>]'
./boost/boost/algorithm/string/split.hpp:67:49:   required from 'SequenceSequenceT& boost::algorithm::find_all(SequenceSequenceT&, Range1T&, const Range2T&) [with SequenceSequenceT = std::vector<boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > > >; Range1T = const std::__cxx11::basic_string<char>; Range2T = std::__cxx11::basic_string<char>]'
pwiz/data/proteome/Digestion.cpp:472:63:   required from here
./boost/boost/function/function_base.hpp:318:54: warning: placement new constructing an object of type 'boost::detail::function::functor_manager_common<boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal> >::functor_type' {aka 'boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>'} and size '12' in a region of type 'char' and size '1' [-Wplacement-new=]
             new (reinterpret_cast<void*>(&out_buffer.data)) functor_type(*in_functor);
                                           ~~~~~~~~~~~^~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:31:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/proteome/Peptide.cpp:31:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/proteome/Peptide.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:27:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/proteome/AminoAcid.cpp:27:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/proteome/AminoAcid.cpp:27:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/minimxml/XMLWriter.cpp:26:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/minimxml/XMLWriter.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from ./boost/boost/iostreams/filtering_stream.hpp:22,
                 from pwiz/utility/minimxml/XMLWriter.cpp:27:
./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)':
./boost/boost/iostreams/chain.hpp:256:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/spirit/home/karma/string.hpp:13,
                 from ./boost/boost/spirit/home/karma.hpp:14,
                 from ./boost/boost/spirit/include/karma.hpp:16,
                 from pwiz/utility/minimxml/XMLWriter.cpp:29:
./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string<String, CharEncoding, Tag, no_attribute>::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const':
./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs]
                 extracted_string_type;
                 ^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:29:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, pwiz::minimxml::SAXParser::Handler&)':
pwiz/utility/minimxml/SAXParser.cpp:431:20: warning: offset '1' outside bounds of constant string [-Warray-bounds]
 PWIZ_API_DECL void parse(istream& is, Handler& handler)
                    ^~~~~
pwiz/utility/minimxml/SAXParser.cpp:517:17: warning: 'inCDATA' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 if (inCDATA)
                 ^~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/Chemistry.cpp:28:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/Chemistry.cpp:28:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/chemistry/Chemistry.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const':
pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/MSIHandler.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/MSIHandler.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/MSIHandler.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/algorithm/string/std_containers_traits.hpp:18,
                 from ./boost/boost/algorithm/string.hpp:18,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
pwiz/utility/misc/Filesystem.cpp:39: warning: "_WIN32_WINNT" redefined
     #define _WIN32_WINNT 0x0400
 
In file included from C:/rtools40/mingw32/i686-w64-mingw32/include/crtdefs.h:10,
                 from C:/rtools40/mingw32/i686-w64-mingw32/include/wchar.h:9,
                 from C:/rtools40/mingw32/include/c++/8.3.0/cwchar:44,
                 from C:/rtools40/mingw32/include/c++/8.3.0/bits/postypes.h:40,
                 from C:/rtools40/mingw32/include/c++/8.3.0/bits/char_traits.h:40,
                 from C:/rtools40/mingw32/include/c++/8.3.0/string:40,
                 from pwiz/utility/misc/String.hpp:27,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw32/i686-w64-mingw32/include/_mingw.h:225: note: this is the location of the previous definition
 #define _WIN32_WINNT 0x502
 
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/range/iterator_range.hpp:13,
                 from ./boost/boost/range/as_literal.hpp:22,
                 from ./boost/boost/algorithm/string/trim.hpp:19,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/TabReader.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/TabReader.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/static_assert.hpp:17,
                 from pwiz/utility/misc/endian.hpp:28,
                 from pwiz/utility/misc/SHA1.cpp:10:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/filesystem/path.hpp:28,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/interprocess/errors.hpp:41,
                 from ./boost/boost/interprocess/exceptions.hpp:24,
                 from ./boost/boost/interprocess/file_mapping.hpp:30,
                 from pwiz/utility/misc/SHA1.cpp:20:
./boost_aux/boost/interprocess/detail/win32_api.hpp: In instantiation of 'static void* boost::interprocess::winapi::function_address_holder<Dummy>::get(unsigned int) [with int Dummy = 0]':
./boost_aux/boost/interprocess/detail/win32_api.hpp:1617:20:   required from here
./boost_aux/boost/interprocess/detail/win32_api.hpp:1544:31: warning: invalid conversion from 'boost::interprocess::winapi::farproc_t' {aka 'int (__attribute__((stdcall)) *)()'} to 'void*' [-fpermissive]
       return FunctionAddresses[id];
              ~~~~~~~~~~~~~~~~~^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/static_assert.hpp:17,
                 from pwiz/utility/misc/endian.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/SHA1Calculator.cpp:33:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/SHA1Calculator.cpp:33:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/SHA1Calculator.cpp:33:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/algorithm/string/replace.hpp:16,
                 from ./boost/boost/date_time/date_facet.hpp:17,
                 from ./boost/boost/date_time/gregorian/gregorian_io.hpp:16,
                 from ./boost/boost/date_time/gregorian/gregorian.hpp:31,
                 from ./boost/boost/date_time/posix_time/time_formatters.hpp:12,
                 from ./boost/boost/date_time/posix_time/posix_time.hpp:24,
                 from ./boost/boost/date_time/local_time/local_time.hpp:11,
                 from pwiz/utility/misc/DateTime.hpp:25,
                 from pwiz/utility/misc/unit.hpp:29,
                 from pwiz/utility/misc/sha1calc.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/unit.hpp:30,
                 from pwiz/utility/misc/sha1calc.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/sha1calc.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c random_access_gzFile.cpp -o random_access_gzFile.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from random_access_gzFile.h:21,
                 from random_access_gzFile.cpp:21:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/path_traits.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/windows_file_codecvt.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/codecvt_error_category.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/thread/src/win32/tss_pe.cpp -o boost/libs/thread/src/win32/tss_pe.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/thread/detail/config.hpp:11,
                 from boost/libs/thread/src/win32/tss_pe.cpp:10:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/thread/src/win32/tss_dll.cpp -o boost/libs/thread/src/win32/tss_dll.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/thread/detail/config.hpp:11,
                 from boost/libs/thread/src/win32/tss_dll.cpp:6:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/thread/src/win32/thread.cpp -o boost/libs/thread/src/win32/thread.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/thread/detail/platform.hpp:14,
                 from ./boost/boost/thread/thread_only.hpp:12,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/thread/detail/thread.hpp:30,
                 from ./boost/boost/thread/thread_only.hpp:22,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/ramp/wglob.cpp -o pwiz/data/msdata/ramp/wglob.o
pwiz/data/msdata/ramp/wglob.cpp: In function 'int glob(const char*, int, int*, glob_t*)':
pwiz/data/msdata/ramp/wglob.cpp:63:9: warning: unused variable 'fileList' [-Wunused-variable]
  char** fileList= NULL;
         ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_aux/boost/nowide/iostream.cpp -o boost_aux/boost/nowide/iostream.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost_aux/boost/nowide/config.hpp:11,
                 from ./boost_aux/boost/nowide/iostream.hpp:11,
                 from boost_aux/boost/nowide/iostream.cpp:9:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/iostream.hpp:12,
                 from boost_aux/boost/nowide/iostream.cpp:9:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/iostream.hpp:12,
                 from boost_aux/boost/nowide/iostream.cpp:9:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
boost_aux/boost/nowide/iostream.cpp: In member function 'virtual int boost::nowide::details::console_input_buffer::underflow()':
boost_aux/boost/nowide/iostream.cpp:189:13: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized]
             if(c==uf::incomplete) {
             ^~
boost_aux/boost/nowide/iostream.cpp:178:28: note: 'c' was declared here
             uf::code_point c;
                            ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c rampR.cpp -o rampR.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from random_access_gzFile.h:21,
                 from ramp.h:72,
                 from rampR.cpp:15:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./pwiz/data/msdata/ramp/wglob.o ./boost_aux/boost/nowide/iostream.o rampR.o -lpthread -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -lws2_32 -lz -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/mzR.buildbin-libdir/00LOCK-mzR/00new/mzR/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mzR'
    finding HTML links ... done
    copyWriteMSData                         html  
    isolationWindow-methods                 html  
    metadata                                html  
    mzR-class                               html  
    finding level-2 HTML links ... done

    openMSfile                              html  
    peaks                                   html  
    pwiz-version                            html  
    writeMSData                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'mzR' ...
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./pwiz/data/msdata/ramp/wglob.o ./boost_aux/boost/nowide/iostream.o rampR.o 
find . -name \*~ -exec rm {} \;   ## from cleanup
find . -name \*.o -exec rm {} \;  ## from cleanup
find . -name "#*#" -exec rm {} \; ## from cleanup
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cramp.cpp -o cramp.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from random_access_gzFile.h:21,
                 from ramp.h:72,
                 from cramp.h:33,
                 from cramp.cpp:49:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from cramp.cpp:49:
cramp.h: In copy constructor 'rampScanInfo::rampScanInfo(rampScanInfo&)':
cramp.h:261:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampScanInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
         memmove(this,&rhs,sizeof(rhs));
                                      ^
In file included from cramp.cpp:49:
cramp.h:251:7: note: 'class rampScanInfo' declared here
 class rampScanInfo: public rampInfo
       ^~~~~~~~~~~~
In file included from cramp.cpp:49:
cramp.h: In copy constructor 'rampRunInfo::rampRunInfo(const rampRunInfo&)':
cramp.h:315:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampRunInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
         memmove(this,&rhs,sizeof(rhs));
                                      ^
cramp.h:305:7: note: 'class rampRunInfo' declared here
 class rampRunInfo: public rampInfo
       ^~~~~~~~~~~
In file included from cramp.cpp:49:
cramp.h: In constructor 'cRamp::cRamp(const char*, bool)':
cramp.h:149:10: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder]
     bool m_declaredScansOnly; // if true, suppress RAMP's habit of adding scans to fill in between declared scans
          ^~~~~~~~~~~~~~~~~~~
cramp.h:148:18: warning:   'rampRunInfo* cRamp::m_runInfo' [-Wreorder]
     rampRunInfo *m_runInfo; // scan count etc
                  ^~~~~~~~~
cramp.cpp:72:1: warning:   when initialized here [-Wreorder]
 cRamp::cRamp( const char* fileName,bool declaredScansOnly ) :
 ^~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ramp_base64.cpp -o ramp_base64.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ramp.cpp -o ramp.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from random_access_gzFile.h:21,
                 from ramp.h:72,
                 from ramp.cpp:44:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
ramp.cpp:248:23: warning: unused variable 'fgot' [-Wunused-variable]
                 char *fgot=ramp_fgets(buf,sizeof(buf)-1,result);
                       ^~~~
ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
ramp.cpp:451:12: warning: unused variable 'nread' [-Wunused-variable]
     size_t nread = ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI);
            ^~~~~
ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
ramp.cpp:650:31: warning: unused variable 'fgot' [-Wunused-variable]
                         char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                               ^~~~
ramp.cpp:692:31: warning: unused variable 'fgot' [-Wunused-variable]
                         char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                               ^~~~
ramp.cpp:729:27: warning: unused variable 'fgot' [-Wunused-variable]
                     char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                           ^~~~
ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
ramp.cpp:1446:27: warning: unused variable 'fgot' [-Wunused-variable]
                     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                           ^~~~
ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:1532:15: warning: unused variable 'fgot' [-Wunused-variable]
         char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
               ^~~~
ramp.cpp:1528:11: warning: unused variable 'fgot' [-Wunused-variable]
     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
           ^~~~
ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:2090:28: warning: unused variable 'nread' [-Wunused-variable]
                     size_t nread = ramp_fread(pData+partial,(int)(peaksLen-partial), pFI);
                            ^~~~~
ramp.cpp:2293:27: warning: unused variable 'fgot' [-Wunused-variable]
                     char *fgot=ramp_fgets(buf, sizeof(buf)-1 , pFI);
                           ^~~~
ramp.cpp:2340:24: warning: unused variable 'nread' [-Wunused-variable]
                 size_t nread = ramp_fread(pData+partial,peaksLen-partial, pFI);
                        ^~~~~
ramp.cpp:2394:21: warning: variable 'err' set but not used [-Wunused-but-set-variable]
                 int err;
                     ^~~
ramp.cpp:2212:19: warning: unused variable 'fgot' [-Wunused-variable]
             char *fgot=ramp_fgets(buf, sizeof(buf)-1, pFI);
                   ^~~~
ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
ramp.cpp:2520:15: warning: unused variable 'fgot' [-Wunused-variable]
         char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
               ^~~~
ramp.cpp:2544:15: warning: unused variable 'fgot' [-Wunused-variable]
         char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
               ^~~~
ramp.cpp:2516:11: warning: unused variable 'fgot' [-Wunused-variable]
     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
           ^~~~
ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
ramp.cpp:2695:19: warning: unused variable 'fgot' [-Wunused-variable]
             char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                   ^~~~
ramp.cpp:2731:19: warning: unused variable 'fgot' [-Wunused-variable]
             char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                   ^~~~
ramp.cpp:2682:11: warning: unused variable 'fgot' [-Wunused-variable]
     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
           ^~~~
ramp.cpp: In function 'int rampSelfTest(char*)':
ramp.cpp:2799:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation]
         strncpy(buf,testname[i],sizeof(buf));
         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ramp.cpp:2812:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation]
         strncpy(buf,filename,sizeof(buf));
         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
ramp.cpp:2816:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation]
         strncpy(buf,filename,sizeof(buf));
         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppRamp.cpp -o RcppRamp.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from random_access_gzFile.h:21,
                 from ramp.h:72,
                 from cramp.h:33,
                 from RcppRamp.h:14,
                 from RcppRamp.cpp:1:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from RcppRamp.h:14,
                 from RcppRamp.cpp:1:
cramp.h: In copy constructor 'rampScanInfo::rampScanInfo(rampScanInfo&)':
cramp.h:261:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampScanInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
         memmove(this,&rhs,sizeof(rhs));
                                      ^
In file included from RcppRamp.h:14,
                 from RcppRamp.cpp:1:
cramp.h:251:7: note: 'class rampScanInfo' declared here
 class rampScanInfo: public rampInfo
       ^~~~~~~~~~~~
In file included from RcppRamp.h:14,
                 from RcppRamp.cpp:1:
cramp.h: In copy constructor 'rampRunInfo::rampRunInfo(const rampRunInfo&)':
cramp.h:315:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampRunInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
         memmove(this,&rhs,sizeof(rhs));
                                      ^
cramp.h:305:7: note: 'class rampRunInfo' declared here
 class rampRunInfo: public rampInfo
       ^~~~~~~~~~~
RcppRamp.cpp: In member function 'Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo()':
RcppRamp.cpp:215:27: warning: unused variable 'info' [-Wunused-variable]
             rampScanInfo *info = ramp->getScanHeaderInfo( 1 );
                           ^~~~
RcppRamp.cpp: In member function 'Rcpp::NumericMatrix RcppRamp::get3DMap(std::vector<int>, double, double, double)':
RcppRamp.cpp:388:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         for (int i = 0; i < scanNumbers.size(); i++)
                         ~~^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppRampModule.cpp -o RcppRampModule.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from random_access_gzFile.h:21,
                 from ramp.h:72,
                 from cramp.h:33,
                 from RcppRamp.h:14,
                 from RcppRampModule.cpp:2:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from RcppRamp.h:14,
                 from RcppRampModule.cpp:2:
cramp.h: In copy constructor 'rampScanInfo::rampScanInfo(rampScanInfo&)':
cramp.h:261:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampScanInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
         memmove(this,&rhs,sizeof(rhs));
                                      ^
In file included from RcppRamp.h:14,
                 from RcppRampModule.cpp:2:
cramp.h:251:7: note: 'class rampScanInfo' declared here
 class rampScanInfo: public rampInfo
       ^~~~~~~~~~~~
In file included from RcppRamp.h:14,
                 from RcppRampModule.cpp:2:
cramp.h: In copy constructor 'rampRunInfo::rampRunInfo(const rampRunInfo&)':
cramp.h:315:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampRunInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
         memmove(this,&rhs,sizeof(rhs));
                                      ^
cramp.h:305:7: note: 'class rampRunInfo' declared here
 class rampRunInfo: public rampInfo
       ^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppPwiz.cpp -o RcppPwiz.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from RcppPwiz.h:12,
                 from RcppPwiz.cpp:1:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Std.hpp:31,
                 from RcppPwiz.h:20,
                 from RcppPwiz.cpp:1:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from pwiz/utility/misc/Std.hpp:32,
                 from RcppPwiz.h:20,
                 from RcppPwiz.cpp:1:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from ./boost/boost/iostreams/filtering_stream.hpp:22,
                 from RcppPwiz.h:23,
                 from RcppPwiz.cpp:1:
./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)':
./boost/boost/iostreams/chain.hpp:256:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getScanHeaderInfo(Rcpp::IntegerVector)':
RcppPwiz.cpp:133:9: warning: unused variable 'N' [-Wunused-variable]
     int N = slp->size();
         ^
RcppPwiz.cpp: In member function 'void RcppPwiz::addSpectrumList(pwiz::msdata::MSData&, Rcpp::DataFrame&, Rcpp::List&, bool)':
RcppPwiz.cpp:745:29: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
     if (precursorScanNum[i] > 0 | precursorMZ[i] > 0) {
RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)':
RcppPwiz.cpp:820:49: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {
                                      ~~~~~~~~~~~^~~~~~~~~~~~~
RcppPwiz.cpp:830:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::msdata::TimeIntensityPair>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
       for (int i = 0; i < pairs.size(); i++) {
                       ~~^~~~~~~~~~~~~~
RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo(Rcpp::IntegerVector)':
RcppPwiz.cpp:850:10: warning: unused variable 'nativeIdFormat_' [-Wunused-variable]
     CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd);
          ^~~~~~~~~~~~~~~
RcppPwiz.cpp: In member function 'Rcpp::NumericMatrix RcppPwiz::get3DMap(std::vector<int>, double, double, double)':
RcppPwiz.cpp:981:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
       for (int i = 0; i < scanNumbers.size(); i++)
                       ~~^~~~~~~~~~~~~~~~~~~~
RcppPwiz.cpp:987:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::msdata::MZIntensityPair>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
    for (int k=0; k < pairs.size(); k++)
                  ~~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppPwizModule.cpp -o RcppPwizModule.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from RcppPwiz.h:12,
                 from RcppPwizModule.cpp:2:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Std.hpp:31,
                 from RcppPwiz.h:20,
                 from RcppPwizModule.cpp:2:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from pwiz/utility/misc/Std.hpp:32,
                 from RcppPwiz.h:20,
                 from RcppPwizModule.cpp:2:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from ./boost/boost/iostreams/filtering_stream.hpp:22,
                 from RcppPwiz.h:23,
                 from RcppPwizModule.cpp:2:
./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)':
./boost/boost/iostreams/chain.hpp:256:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppIdent.cpp -o RcppIdent.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Std.hpp:31,
                 from RcppIdent.h:14,
                 from RcppIdent.cpp:1:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from pwiz/utility/misc/Std.hpp:32,
                 from RcppIdent.h:14,
                 from RcppIdent.cpp:1:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
RcppIdent.cpp: In member function 'Rcpp::DataFrame RcppIdent::getScore()':
RcppIdent.cpp:293:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    for (size_t j = 0; j < nCvParams; j++) {
                       ~~^~~~~~~~~~~
RcppIdent.cpp: In member function 'Rcpp::List RcppIdent::getPara()':
RcppIdent.cpp:382:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::data::CVParam>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 0 ; i < sip[0]->additionalSearchParams.cvParams.size(); i++)
                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RcppIdent.cpp:388:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::data::UserParam>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++)
                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppIdentModule.cpp -o RcppIdentModule.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Std.hpp:31,
                 from RcppIdent.h:14,
                 from RcppIdentModule.cpp:2:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from pwiz/utility/misc/Std.hpp:32,
                 from RcppIdent.h:14,
                 from RcppIdentModule.cpp:2:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/system/config.hpp:13,
                 from ./boost/boost/system/error_code.hpp:14,
                 from boost/libs/system/src/error_code.cpp:16:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/posix_api.cpp:21:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/fileiter.cpp -o boost/libs/regex/src/fileiter.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/fileiter.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex_raw_buffer.cpp -o boost/libs/regex/src/regex_raw_buffer.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/regex_raw_buffer.cpp:21:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/cregex.cpp -o boost/libs/regex/src/cregex.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from ./boost/boost/regex.hpp:28,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/regex_debug.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/instances.cpp -o boost/libs/regex/src/instances.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/instances.cpp:21:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/icu.cpp -o boost/libs/regex/src/icu.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/icu.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/usinstances.cpp -o boost/libs/regex/src/usinstances.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/detail/workaround.hpp:41,
                 from boost/libs/regex/src/usinstances.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/regex.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/wide_posix_api.cpp:21:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex_traits_defaults.cpp -o boost/libs/regex/src/regex_traits_defaults.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from ./boost/boost/regex/regex_traits.hpp:23,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/winstances.cpp -o boost/libs/regex/src/winstances.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/winstances.cpp:21:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/wc_regex_traits.cpp -o boost/libs/regex/src/wc_regex_traits.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/detail/workaround.hpp:41,
                 from boost/libs/regex/src/wc_regex_traits.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/c_regex_traits.cpp -o boost/libs/regex/src/c_regex_traits.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/c_regex_traits.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/cpp_regex_traits.cpp -o boost/libs/regex/src/cpp_regex_traits.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/regex/src/static_mutex.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/w32_regex_traits.cpp -o boost/libs/regex/src/w32_regex_traits.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/w32_regex_traits.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/range/iterator_range.hpp:13,
                 from ./boost/boost/iostreams/traits.hpp:39,
                 from ./boost/boost/iostreams/detail/dispatch.hpp:17,
                 from ./boost/boost/iostreams/read.hpp:19,
                 from ./boost/boost/iostreams/detail/buffer.hpp:20,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:49,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/iostreams/src/file_descriptor.cpp:16:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/filesystem/operations.hpp:18,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/filesystem/path.hpp:28,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
In file included from ./boost/boost/config.hpp:57,
                 from boost/libs/filesystem/src/path.cpp:12:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/filesystem/path.hpp:28,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/utf8_codecvt_facet.cpp:15:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/chrono/config.hpp:15,
                 from ./boost/boost/chrono/duration.hpp:33,
                 from ./boost/boost/chrono/chrono.hpp:11,
                 from ./boost/boost/chrono/detail/inlined/chrono.hpp:13,
                 from boost/libs/chrono/src/chrono.cpp:14:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/chrono/config.hpp:15,
                 from ./boost/boost/chrono/detail/inlined/process_cpu_clocks.hpp:15,
                 from boost/libs/chrono/src/process_cpu_clocks.cpp:17:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/chrono/config.hpp:15,
                 from ./boost/boost/chrono/detail/inlined/thread_clock.hpp:14,
                 from boost/libs/chrono/src/thread_clock.cpp:18:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/MemoryIndex.cpp:26:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/MemoryIndex.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/common/MemoryIndex.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/checked_delete.hpp:15,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:26,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::MemoryIndex::Impl]':
./boost/boost/smart_ptr/detail/shared_count.hpp:134:34:   required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::MemoryIndex::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:271:20:   required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::data::MemoryIndex::Impl; Y = pwiz::data::MemoryIndex::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:349:44:   required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::data::MemoryIndex::Impl; T = pwiz::data::MemoryIndex::Impl]'
pwiz/data/common/MemoryIndex.cpp:73:58:   required from here
./boost/boost/core/checked_delete.hpp:34:5: warning: deleting object of polymorphic class type 'pwiz::data::MemoryIndex::Impl' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete x;
     ^~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/range/iterator_range.hpp:13,
                 from ./boost/boost/range/as_literal.hpp:22,
                 from ./boost/boost/algorithm/string/predicate.hpp:19,
                 from pwiz/data/common/CVTranslator.cpp:28:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:29:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/common/CVTranslator.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)':
pwiz/data/common/CVTranslator.cpp:133:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:135:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:136:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/common/cv.cpp:34:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from pwiz/data/common/cv.cpp:24765:
pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)':
pwiz/data/common/cv.inl:102:23: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
         for (int o=0;o<oboPrefixesSize_;++o)
                      ~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/ParamTypes.cpp:28:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/common/ParamTypes.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/spirit/home/karma/string.hpp:13,
                 from ./boost/boost/spirit/home/karma.hpp:14,
                 from ./boost/boost/spirit/include/karma.hpp:16,
                 from pwiz/data/common/ParamTypes.cpp:29:
./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string<String, CharEncoding, Tag, no_attribute>::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const':
./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs]
                 extracted_string_type;
                 ^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.cpp:26:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/common/BinaryIndexStream.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/common/BinaryIndexStream.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
In file included from ./boost/boost/checked_delete.hpp:15,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:26,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::BinaryIndexStream::Impl]':
./boost/boost/smart_ptr/detail/shared_count.hpp:134:34:   required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:271:20:   required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::data::BinaryIndexStream::Impl; Y = pwiz::data::BinaryIndexStream::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:349:44:   required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl; T = pwiz::data::BinaryIndexStream::Impl]'
pwiz/data/common/BinaryIndexStream.cpp:402:103:   required from here
./boost/boost/core/checked_delete.hpp:34:5: warning: deleting object of polymorphic class type 'pwiz::data::BinaryIndexStream::Impl' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete x;
     ^~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from pwiz/data/common/diff_std.cpp:27:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost_aux/boost/enum/iterator.hpp:18,
                 from ./boost_aux/boost/enum.hpp:18,
                 from pwiz/data/common/Unimod.hpp:31,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost_aux/boost/enum/bitfield.hpp:22,
                 from ./boost_aux/boost/enum.hpp:20,
                 from pwiz/data/common/Unimod.hpp:31,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/common/Unimod.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/function/detail/maybe_include.hpp:23,
                 from ./boost/boost/function/detail/function_iterate.hpp:14,
                 from ./boost/boost/preprocessor/iteration/detail/iter/forward1.hpp:57,
                 from ./boost/boost/function.hpp:64,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost_aux/boost/enum/bitfield.hpp:22,
                 from ./boost_aux/boost/enum.hpp:20,
                 from pwiz/data/common/Unimod.hpp:31,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/function/function_template.hpp: In instantiation of 'void boost::detail::function::basic_vtable2<R, T0, T1>::assign_functor(FunctionObj, boost::detail::function::function_buffer&, mpl_::true_) const [with FunctionObj = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; mpl_::true_ = mpl_::bool_<true>]':
./boost/boost/function/function_template.hpp:608:13:   required from 'bool boost::detail::function::basic_vtable2<R, T0, T1>::assign_to(FunctionObj, boost::detail::function::function_buffer&, boost::detail::function::function_obj_tag) const [with FunctionObj = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:498:45:   required from 'bool boost::detail::function::basic_vtable2<R, T0, T1>::assign_to(F, boost::detail::function::function_buffer&) const [with F = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:942:7:   required from 'void boost::function2<R, T1, T2>::assign_to(Functor) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:728:7:   required from 'boost::function2<R, T1, T2>::function2(Functor, typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type = int]'
./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36:   required from 'boost::algorithm::detail::find_iterator_base<IteratorT>::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/find_iterator.hpp:265:29:   required from 'boost::algorithm::split_iterator<IteratorT>::split_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/iter_find.hpp:170:21:   required from 'SequenceSequenceT& boost::algorithm::iter_split(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector<std::__cxx11::basic_string<char> >; RangeT = const std::__cxx11::basic_string<char>; FinderT = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>]'
./boost/boost/algorithm/string/split.hpp:146:50:   required from 'SequenceSequenceT& boost::algorithm::split(SequenceSequenceT&, RangeT&, PredicateT, boost::algorithm::token_compress_mode_type) [with SequenceSequenceT = std::vector<std::__cxx11::basic_string<char> >; RangeT = const std::__cxx11::basic_string<char>; PredicateT = boost::algorithm::detail::is_classifiedF]'
pwiz/data/common/Unimod.cpp:129:71:   required from here
./boost/boost/function/function_template.hpp:572:49: warning: placement new constructing an object of type 'boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>' and size '24' in a region of type 'char' and size '1' [-Wplacement-new=]
           new (reinterpret_cast<void*>(&functor.data)) FunctionObj(f);
                                         ~~~~~~~~^~~~
In file included from ./boost/boost/function/detail/prologue.hpp:17,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost_aux/boost/enum/bitfield.hpp:22,
                 from ./boost_aux/boost/enum.hpp:20,
                 from pwiz/data/common/Unimod.hpp:31,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/boost/function/function_base.hpp: In instantiation of 'static void boost::detail::function::functor_manager_common<Functor>::manage_small(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>]':
./boost/boost/function/function_base.hpp:364:56:   required from 'static void boost::detail::function::functor_manager<Functor>::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, mpl_::true_) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; mpl_::true_ = mpl_::bool_<true>]'
./boost/boost/function/function_base.hpp:412:18:   required from 'static void boost::detail::function::functor_manager<Functor>::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, boost::detail::function::function_obj_tag) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>]'
./boost/boost/function/function_base.hpp:440:20:   required from 'static void boost::detail::function::functor_manager<Functor>::manage(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>]'
./boost/boost/function/function_template.hpp:940:13:   required from 'void boost::function2<R, T1, T2>::assign_to(Functor) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:728:7:   required from 'boost::function2<R, T1, T2>::function2(Functor, typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type) [with Functor = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type = int]'
./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36:   required from 'boost::algorithm::detail::find_iterator_base<IteratorT>::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/find_iterator.hpp:265:29:   required from 'boost::algorithm::split_iterator<IteratorT>::split_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/iter_find.hpp:170:21:   required from 'SequenceSequenceT& boost::algorithm::iter_split(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector<std::__cxx11::basic_string<char> >; RangeT = const std::__cxx11::basic_string<char>; FinderT = boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>]'
./boost/boost/algorithm/string/split.hpp:146:50:   required from 'SequenceSequenceT& boost::algorithm::split(SequenceSequenceT&, RangeT&, PredicateT, boost::algorithm::token_compress_mode_type) [with SequenceSequenceT = std::vector<std::__cxx11::basic_string<char> >; RangeT = const std::__cxx11::basic_string<char>; PredicateT = boost::algorithm::detail::is_classifiedF]'
pwiz/data/common/Unimod.cpp:129:71:   required from here
./boost/boost/function/function_base.hpp:318:54: warning: placement new constructing an object of type 'boost::detail::function::functor_manager_common<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF> >::functor_type' {aka 'boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>'} and size '24' in a region of type 'char' and size '1' [-Wplacement-new=]
             new (reinterpret_cast<void*>(&out_buffer.data)) functor_type(*in_functor);
                                           ~~~~~~~~~~~^~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/smart_ptr.hpp:19,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/smart_ptr.hpp:19,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/smart_ptr.hpp:19,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/smart_ptr.hpp:19,
                 from ./pwiz/data/msdata/SpectrumWorkerThreads.hpp:27,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:28:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:29:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:29:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:31:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/examples.cpp:26:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/examples.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mzML.cpp:33:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Serializer_mzML.cpp:33:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.cpp:28:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Serializer_MSn.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/msdata/Reader.cpp:27:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Reader.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.cpp:27:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Serializer_MGF.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/spirit/home/karma/string.hpp:13,
                 from ./boost/boost/spirit/home/karma.hpp:14,
                 from ./boost/boost/spirit/include/karma.hpp:16,
                 from pwiz/data/msdata/Serializer_MGF.cpp:29:
./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string<String, CharEncoding, Tag, no_attribute>::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const':
./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs]
                 extracted_string_type;
                 ^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:33:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:34:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:30:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:30:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:32:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:32:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:28:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:31:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:31:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:29:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:29:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/range/iterator_range.hpp:13,
                 from ./boost/boost/iostreams/traits.hpp:39,
                 from ./boost/boost/iostreams/pipeline.hpp:18,
                 from ./boost/boost/iostreams/detail/push.hpp:22,
                 from ./boost/boost/iostreams/chain.hpp:29,
                 from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:30:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:30:
./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)':
./boost/boost/iostreams/chain.hpp:256:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/iostreams/copy.hpp:26,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:32:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:38:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::__cxx11::string&, size_t*)':
pwiz/data/msdata/BinaryDataEncoder.cpp:280:37: warning: 'byteCount' may be used uninitialized in this function [-Wmaybe-uninitialized]
         filterArray<zlib_compressor>(byteBuffer, byteCount,compressed);
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/BinaryDataEncoder.cpp:280:37: warning: 'byteBuffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Diff.cpp:28:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Diff.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/MSData.cpp:26:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/MSData.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/References.cpp:26:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/References.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:29:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:30:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/msdata/SpectrumList_mzXML.cpp: In constructor 'pwiz::msdata::{anonymous}::SpectrumList_mzXMLImpl::SpectrumList_mzXMLImpl(boost::shared_ptr<std::basic_istream<char> >, const pwiz::msdata::MSData&, bool)':
pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=]
     } catch (index_not_found e){
                              ^
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:30:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/msdata/IO.cpp:29:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/IO.cpp:30:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerBinaryDataArray::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:1727:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
                 if (!dataProcessingRef.empty())
                 ^~
pwiz/data/msdata/IO.cpp:1730:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
                     getAttribute(attributes, "encodedLength", encodedLength_, NoXMLUnescape);
                     ^~~~~~~~~~~~
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2020:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList")
                      ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2731:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
         else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
                  ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:29:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:30:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:30:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumInfo.cpp:29:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumInfo.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:27:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/RAMPAdapter.cpp:31:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/RAMPAdapter.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)',
    inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:283:25:
pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation]
     strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH);
     ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)',
    inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:284:25:
pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation]
     strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH);
     ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)',
    inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:285:25:
pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation]
     strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH);
     ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)',
    inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:286:25:
pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation]
     strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH);
     ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/LegacyAdapter.cpp:31:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/LegacyAdapter.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumIterator.cpp:29:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumIterator.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::equal(const pwiz::msdata::SpectrumIterator::Impl&) const':
pwiz/data/msdata/SpectrumIterator.cpp:125:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return (done() && &that.spectrumList_==&pastEndMarker_ ||
             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_);
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::done() const':
pwiz/data/msdata/SpectrumIterator.cpp:141:34: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
            ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:36:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/MSDataFile.cpp:37:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from ./boost/boost/iostreams/filtering_stream.hpp:22,
                 from pwiz/data/msdata/MSDataFile.cpp:41:
./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)':
./boost/boost/iostreams/chain.hpp:256:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)':
pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
     } else if (init == mask) {
                ~~~~~^~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/multi_index/sequenced_index.hpp:49,
                 from ./pwiz/utility/misc/mru_list.hpp:30,
                 from pwiz/data/msdata/MemoryMRUCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.hpp:28,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumListCache.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/Index_mzML.cpp:25:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/Index_mzML.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:28:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:28:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:30:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/IdentDataFile.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from ./boost/boost/iostreams/filtering_stream.hpp:22,
                 from pwiz/data/identdata/IdentDataFile.cpp:34:
./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)':
./boost/boost/iostreams/chain.hpp:256:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/identdata/Reader.cpp:27:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/Reader.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/Serializer_protXML.cpp:31:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/Serializer_protXML.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/identdata/Serializer_protXML.cpp: In constructor 'pwiz::identdata::{anonymous}::Handler_protXML::Handler_protXML(pwiz::identdata::IdentData&, const pwiz::util::IterationListenerRegistry*, bool, std::vector<std::__cxx11::basic_string<char> >*)':
pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: 'pwiz::identdata::{anonymous}::Handler_protXML::strict' will be initialized after [-Wreorder]
     bool strict;
          ^~~~~~
pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning:   'int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides' [-Wreorder]
     int nPeptides;
         ^~~~~~~~~
pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning:   when initialized here [-Wreorder]
     Handler_protXML(IdentData& mzid,
     ^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:28:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/identdata/Serializer_pepXML.cpp: In function 'void pwiz::identdata::{anonymous}::write_spectrum_queries(pwiz::minimxml::XMLWriter&, const pwiz::identdata::IdentData&, const string&, const pwiz::util::IterationListenerRegistry*)':
pwiz/data/identdata/Serializer_pepXML.cpp:800:52: warning: 'lastSpectrumIndex' may be used uninitialized in this function [-Wmaybe-uninitialized]
             if (sii.chargeState != lastChargeState || spectrumIndex != lastSpectrumIndex)
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/Serializer_mzid.cpp:30:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/Serializer_mzid.cpp:30:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/identdata/IO.cpp:30:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/IO.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/identdata/IdentData.hpp:31,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/References.cpp:27:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/References.cpp:27:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/identdata/References.cpp: In function 'void pwiz::identdata::References::resolve(std::vector<boost::shared_ptr<pwiz::identdata::Contact> >&, pwiz::identdata::IdentData&)':
pwiz/data/identdata/References.cpp:148:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
         else if (dynamic_cast<Person*>(c.get()))
                 ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/proteome/Modification.cpp:30:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/proteome/Modification.cpp:30:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/proteome/Modification.cpp:30:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/proteome/Modification.cpp:89:5: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     auto_ptr<Formula> formula_;
     ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/proteome/Digestion.cpp:32:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:32:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/proteome/Digestion.cpp:32:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/function/detail/maybe_include.hpp:23,
                 from ./boost/boost/function/detail/function_iterate.hpp:14,
                 from ./boost/boost/preprocessor/iteration/detail/iter/forward1.hpp:57,
                 from ./boost/boost/function.hpp:64,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:32:
./boost/boost/function/function_template.hpp: In instantiation of 'void boost::detail::function::basic_vtable2<R, T0, T1>::assign_functor(FunctionObj, boost::detail::function::function_buffer&, mpl_::true_) const [with FunctionObj = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; mpl_::true_ = mpl_::bool_<true>]':
./boost/boost/function/function_template.hpp:608:13:   required from 'bool boost::detail::function::basic_vtable2<R, T0, T1>::assign_to(FunctionObj, boost::detail::function::function_buffer&, boost::detail::function::function_obj_tag) const [with FunctionObj = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:498:45:   required from 'bool boost::detail::function::basic_vtable2<R, T0, T1>::assign_to(F, boost::detail::function::function_buffer&) const [with F = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:942:7:   required from 'void boost::function2<R, T1, T2>::assign_to(Functor) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:728:7:   required from 'boost::function2<R, T1, T2>::function2(Functor, typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type = int]'
./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36:   required from 'boost::algorithm::detail::find_iterator_base<IteratorT>::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/find_iterator.hpp:100:26:   required from 'boost::algorithm::find_iterator<IteratorT>::find_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/iter_find.hpp:100:21:   required from 'SequenceSequenceT& boost::algorithm::iter_find(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector<boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > > >; RangeT = const std::__cxx11::basic_string<char>; FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>]'
./boost/boost/algorithm/string/split.hpp:67:49:   required from 'SequenceSequenceT& boost::algorithm::find_all(SequenceSequenceT&, Range1T&, const Range2T&) [with SequenceSequenceT = std::vector<boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > > >; Range1T = const std::__cxx11::basic_string<char>; Range2T = std::__cxx11::basic_string<char>]'
pwiz/data/proteome/Digestion.cpp:472:63:   required from here
./boost/boost/function/function_template.hpp:572:49: warning: placement new constructing an object of type 'boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>' and size '24' in a region of type 'char' and size '1' [-Wplacement-new=]
           new (reinterpret_cast<void*>(&functor.data)) FunctionObj(f);
                                         ~~~~~~~~^~~~
In file included from ./boost/boost/function/detail/prologue.hpp:17,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:32:
./boost/boost/function/function_base.hpp: In instantiation of 'static void boost::detail::function::functor_manager_common<Functor>::manage_small(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>]':
./boost/boost/function/function_base.hpp:364:56:   required from 'static void boost::detail::function::functor_manager<Functor>::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, mpl_::true_) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; mpl_::true_ = mpl_::bool_<true>]'
./boost/boost/function/function_base.hpp:412:18:   required from 'static void boost::detail::function::functor_manager<Functor>::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, boost::detail::function::function_obj_tag) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>]'
./boost/boost/function/function_base.hpp:440:20:   required from 'static void boost::detail::function::functor_manager<Functor>::manage(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>]'
./boost/boost/function/function_template.hpp:940:13:   required from 'void boost::function2<R, T1, T2>::assign_to(Functor) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/function/function_template.hpp:728:7:   required from 'boost::function2<R, T1, T2>::function2(Functor, typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > >; T0 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; T1 = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; typename boost::enable_if_c<boost::type_traits::ice_not<boost::is_integral<Functor>::value>::value, int>::type = int]'
./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36:   required from 'boost::algorithm::detail::find_iterator_base<IteratorT>::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/find_iterator.hpp:100:26:   required from 'boost::algorithm::find_iterator<IteratorT>::find_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >]'
./boost/boost/algorithm/string/iter_find.hpp:100:21:   required from 'SequenceSequenceT& boost::algorithm::iter_find(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector<boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > > >; RangeT = const std::__cxx11::basic_string<char>; FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>]'
./boost/boost/algorithm/string/split.hpp:67:49:   required from 'SequenceSequenceT& boost::algorithm::find_all(SequenceSequenceT&, Range1T&, const Range2T&) [with SequenceSequenceT = std::vector<boost::iterator_range<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> > > >; Range1T = const std::__cxx11::basic_string<char>; Range2T = std::__cxx11::basic_string<char>]'
pwiz/data/proteome/Digestion.cpp:472:63:   required from here
./boost/boost/function/function_base.hpp:318:54: warning: placement new constructing an object of type 'boost::detail::function::functor_manager_common<boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal> >::functor_type' {aka 'boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >, boost::algorithm::is_equal>'} and size '24' in a region of type 'char' and size '1' [-Wplacement-new=]
             new (reinterpret_cast<void*>(&out_buffer.data)) functor_type(*in_functor);
                                           ~~~~~~~~~~~^~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:31:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/proteome/Peptide.cpp:31:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/proteome/Peptide.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:27:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/proteome/AminoAcid.cpp:27:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/proteome/AminoAcid.cpp:27:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/minimxml/XMLWriter.cpp:26:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/minimxml/XMLWriter.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 from ./boost/boost/iostreams/filtering_stream.hpp:22,
                 from pwiz/utility/minimxml/XMLWriter.cpp:27:
./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)':
./boost/boost/iostreams/chain.hpp:256:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/spirit/home/karma/string.hpp:13,
                 from ./boost/boost/spirit/home/karma.hpp:14,
                 from ./boost/boost/spirit/include/karma.hpp:16,
                 from pwiz/utility/minimxml/XMLWriter.cpp:29:
./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string<String, CharEncoding, Tag, no_attribute>::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const':
./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs]
                 extracted_string_type;
                 ^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:29:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:29:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, pwiz::minimxml::SAXParser::Handler&)':
pwiz/utility/minimxml/SAXParser.cpp:431:20: warning: offset '1' outside bounds of constant string [-Warray-bounds]
 PWIZ_API_DECL void parse(istream& is, Handler& handler)
                    ^~~~~
pwiz/utility/minimxml/SAXParser.cpp:517:17: warning: 'inCDATA' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 if (inCDATA)
                 ^~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/Chemistry.cpp:28:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/Chemistry.cpp:28:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/chemistry/Chemistry.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const':
pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/MSIHandler.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/MSIHandler.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/MSIHandler.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/algorithm/string/std_containers_traits.hpp:18,
                 from ./boost/boost/algorithm/string.hpp:18,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
pwiz/utility/misc/Filesystem.cpp:39: warning: "_WIN32_WINNT" redefined
     #define _WIN32_WINNT 0x0400
 
In file included from C:/rtools40/mingw64/x86_64-w64-mingw32/include/crtdefs.h:10,
                 from C:/rtools40/mingw64/x86_64-w64-mingw32/include/wchar.h:9,
                 from C:/rtools40/mingw64/include/c++/8.3.0/cwchar:44,
                 from C:/rtools40/mingw64/include/c++/8.3.0/bits/postypes.h:40,
                 from C:/rtools40/mingw64/include/c++/8.3.0/bits/char_traits.h:40,
                 from C:/rtools40/mingw64/include/c++/8.3.0/string:40,
                 from pwiz/utility/misc/String.hpp:27,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/_mingw.h:225: note: this is the location of the previous definition
 #define _WIN32_WINNT 0x502
 
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/range/iterator_range.hpp:13,
                 from ./boost/boost/range/as_literal.hpp:22,
                 from ./boost/boost/algorithm/string/trim.hpp:19,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from pwiz/utility/misc/String.hpp:30,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/TabReader.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/TabReader.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83:
./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)':
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/shared_mutex.hpp:18,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&new_value),
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/static_assert.hpp:17,
                 from pwiz/utility/misc/endian.hpp:28,
                 from pwiz/utility/misc/SHA1.cpp:10:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/filesystem/path.hpp:28,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/interprocess/errors.hpp:41,
                 from ./boost/boost/interprocess/exceptions.hpp:24,
                 from ./boost/boost/interprocess/file_mapping.hpp:30,
                 from pwiz/utility/misc/SHA1.cpp:20:
./boost_aux/boost/interprocess/detail/win32_api.hpp: In instantiation of 'static void* boost::interprocess::winapi::function_address_holder<Dummy>::get(unsigned int) [with int Dummy = 0]':
./boost_aux/boost/interprocess/detail/win32_api.hpp:1617:20:   required from here
./boost_aux/boost/interprocess/detail/win32_api.hpp:1544:31: warning: invalid conversion from 'boost::interprocess::winapi::farproc_t' {aka 'long long int (*)()'} to 'void*' [-fpermissive]
       return FunctionAddresses[id];
              ~~~~~~~~~~~~~~~~~^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/static_assert.hpp:17,
                 from pwiz/utility/misc/endian.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:25:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/lexical_cast.hpp:30,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/SHA1Calculator.cpp:33:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/SHA1Calculator.cpp:33:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/SHA1Calculator.cpp:33:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/boost/mpl/arg.hpp:25,
                 from ./boost/boost/mpl/placeholders.hpp:24,
                 from ./boost/boost/iterator/iterator_categories.hpp:17,
                 from ./boost/boost/iterator/iterator_facade.hpp:14,
                 from ./boost/boost/range/iterator_range_core.hpp:27,
                 from ./boost/boost/algorithm/string/replace.hpp:16,
                 from ./boost/boost/date_time/date_facet.hpp:17,
                 from ./boost/boost/date_time/gregorian/gregorian_io.hpp:16,
                 from ./boost/boost/date_time/gregorian/gregorian.hpp:31,
                 from ./boost/boost/date_time/posix_time/time_formatters.hpp:12,
                 from ./boost/boost/date_time/posix_time/posix_time.hpp:24,
                 from ./boost/boost/date_time/local_time/local_time.hpp:11,
                 from pwiz/utility/misc/DateTime.hpp:25,
                 from pwiz/utility/misc/unit.hpp:29,
                 from pwiz/utility/misc/sha1calc.cpp:25:
./boost/boost/mpl/assert.hpp: At global scope:
./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/unit.hpp:30,
                 from pwiz/utility/misc/sha1calc.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/sha1calc.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c random_access_gzFile.cpp -o random_access_gzFile.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from random_access_gzFile.h:21,
                 from random_access_gzFile.cpp:21:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/path_traits.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/windows_file_codecvt.cpp:20:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/codecvt_error_category.cpp:22:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/thread/src/win32/tss_pe.cpp -o boost/libs/thread/src/win32/tss_pe.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/thread/detail/config.hpp:11,
                 from boost/libs/thread/src/win32/tss_pe.cpp:10:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/thread/src/win32/tss_dll.cpp -o boost/libs/thread/src/win32/tss_dll.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/thread/detail/config.hpp:11,
                 from boost/libs/thread/src/win32/tss_dll.cpp:6:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost/libs/thread/src/win32/thread.cpp -o boost/libs/thread/src/win32/thread.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/thread/detail/platform.hpp:14,
                 from ./boost/boost/thread/thread_only.hpp:12,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/thread/detail/thread.hpp:30,
                 from ./boost/boost/thread/thread_only.hpp:22,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/win32/thread_data.hpp:10,
                 from ./boost/boost/thread/thread_only.hpp:15,
                 from boost/libs/thread/src/win32/thread.cpp:17:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/ramp/wglob.cpp -o pwiz/data/msdata/ramp/wglob.o
pwiz/data/msdata/ramp/wglob.cpp: In function 'int glob(const char*, int, int*, glob_t*)':
pwiz/data/msdata/ramp/wglob.cpp:63:9: warning: unused variable 'fileList' [-Wunused-variable]
  char** fileList= NULL;
         ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_aux/boost/nowide/iostream.cpp -o boost_aux/boost/nowide/iostream.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost_aux/boost/nowide/config.hpp:11,
                 from ./boost_aux/boost/nowide/iostream.hpp:11,
                 from boost_aux/boost/nowide/iostream.cpp:9:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/iostream.hpp:12,
                 from boost_aux/boost/nowide/iostream.cpp:9:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/iostream.hpp:12,
                 from boost_aux/boost/nowide/iostream.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
boost_aux/boost/nowide/iostream.cpp: In member function 'virtual int boost::nowide::details::console_input_buffer::underflow()':
boost_aux/boost/nowide/iostream.cpp:189:13: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized]
             if(c==uf::incomplete) {
             ^~
boost_aux/boost/nowide/iostream.cpp:178:28: note: 'c' was declared here
             uf::code_point c;
                            ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c rampR.cpp -o rampR.o
In file included from ./boost/boost/config.hpp:57,
                 from ./boost/boost/iostreams/positioning.hpp:18,
                 from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from random_access_gzFile.h:21,
                 from ramp.h:72,
                 from rampR.cpp:15:
./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 
<command-line>: note: this is the location of the previous definition
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./pwiz/data/msdata/ramp/wglob.o ./boost_aux/boost/nowide/iostream.o rampR.o -lpthread -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -lws2_32 -lz -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/mzR.buildbin-libdir/mzR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mzR' as mzR_2.24.1.zip
* DONE (mzR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'mzR' successfully unpacked and MD5 sums checked

Tests output

mzR.Rcheck/tests_i386/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("mzR")
Loading required package: Rcpp
> library("msdata")
> 
> BiocGenerics:::testPackage("mzR")
Loading required namespace: XML
reading Tandem.mzid.gz... DONE!
Mass Spectrometry file handle.
Filename:  MM14.mzML 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  threonine_i2_e35_pH_tree.mzXML 
Number of scans:  55 
Mass Spectrometry file handle.
Filename:  MM14.mzdata 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  MM14.mzdata.gz 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  MM14.mzML 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  threonine_i2_e35_pH_tree.mzXML 
Number of scans:  55 
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].


RUNIT TEST PROTOCOL -- Thu May 06 05:05:21 2021 
*********************************************** 
Number of test functions: 39 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mzR RUnit Tests - 39 test functions, 0 errors, 0 failures
Number of test functions: 39 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: pwiz not yet initialized. 
2: pwiz not yet initialized. 
> 
> proc.time()
   user  system elapsed 
  42.18    5.65   60.29

mzR.Rcheck/tests_x64/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("mzR")
Loading required package: Rcpp
> library("msdata")
> 
> BiocGenerics:::testPackage("mzR")
Loading required namespace: XML
reading Tandem.mzid.gz... DONE!
Mass Spectrometry file handle.
Filename:  MM14.mzML 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  threonine_i2_e35_pH_tree.mzXML 
Number of scans:  55 
Mass Spectrometry file handle.
Filename:  MM14.mzdata 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  MM14.mzdata.gz 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  MM14.mzML 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  threonine_i2_e35_pH_tree.mzXML 
Number of scans:  55 
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].


RUNIT TEST PROTOCOL -- Thu May 06 05:06:16 2021 
*********************************************** 
Number of test functions: 39 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mzR RUnit Tests - 39 test functions, 0 errors, 0 failures
Number of test functions: 39 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: pwiz not yet initialized. 
2: pwiz not yet initialized. 
> 
> proc.time()
   user  system elapsed 
  40.62    4.45   54.93

Example timings

mzR.Rcheck/examples_i386/mzR-Ex.timings

nameusersystemelapsed
copyWriteMSData0.140.080.30
isolationWindow-methods1.610.141.75
metadata1.410.613.50
mzR-class0.030.030.06
openMSfile1.280.581.86
peaks1.200.091.30
writeMSData0.080.020.09

mzR.Rcheck/examples_x64/mzR-Ex.timings

nameusersystemelapsed
copyWriteMSData0.120.030.16
isolationWindow-methods1.40.21.6
metadata0.820.561.41
mzR-class0.060.020.08
openMSfile0.890.481.37
peaks1.150.081.22
writeMSData0.10.00.1