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BUILD BIN 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: 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
StartedAt: 2021-05-06 09:37:18 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 09:59:09 -0400 (Thu, 06 May 2021)
EllapsedTime: 1310.8 seconds
RetCode: 0
Status:   OK   
PackageFile: mzR_2.24.1.zip
PackageFileSize: 7.543 MiB

Command output

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###
### Running command:
###
###   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
###
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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