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This page was generated on 2022-11-26 11:05:44 -0500 (Sat, 26 Nov 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4503
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4277
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4309
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for mzR on nebbiolo2


To the developers/maintainers of the mzR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mzR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1319/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mzR 2.32.0  (landing page)
Steffen Neumann
Snapshot Date: 2022-11-25 14:00:04 -0500 (Fri, 25 Nov 2022)
git_url: https://git.bioconductor.org/packages/mzR
git_branch: RELEASE_3_16
git_last_commit: ef57d59
git_last_commit_date: 2022-11-01 11:06:10 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: mzR
Version: 2.32.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:mzR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings mzR_2.32.0.tar.gz
StartedAt: 2022-11-25 22:13:02 -0500 (Fri, 25 Nov 2022)
EndedAt: 2022-11-25 22:14:25 -0500 (Fri, 25 Nov 2022)
EllapsedTime: 82.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: mzR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:mzR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings mzR_2.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/mzR.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘mzR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzR’ version ‘2.32.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mzR’ can be installed ... WARNING
Found the following significant warnings:
  pwiz/data/msdata/MSData.cpp:1086:20: warning: control reaches end of non-void function [-Wreturn-type]
  pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type ‘struct pwiz::msdata::SpectrumList_mzXML::index_not_found’ by value [-Wcatch-value=]
  pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: ‘pwiz::identdata::{anonymous}::Handler_protXML::strict’ will be initialized after [-Wreorder]
  pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning:   ‘int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides’ [-Wreorder]
  pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning:   when initialized here [-Wreorder]
  pwiz/data/proteome/Modification.cpp:89:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
See ‘/home/biocbuild/bbs-3.16-bioc/meat/mzR.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 159.8Mb
  sub-directories of 1Mb or more:
    libs  159.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.16-bioc/R/library/mzR/libs/mzR.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘mzR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/mzR.Rcheck/00check.log’
for details.



Installation output

mzR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL mzR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘mzR’ ...
** using staged installation
** libs
rm -f 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/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_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/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/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.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/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/BinaryData.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 ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppPwiz.cpp -o RcppPwiz.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from RcppPwiz.h:12,
                 from RcppPwiz.cpp:1:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from pwiz/data/msdata/Reader.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:30,
                 from RcppPwiz.h:12,
                 from RcppPwiz.cpp:1:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RcppPwiz.cpp: In member function ‘Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector)’:
RcppPwiz.cpp:407:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  407 |       if (current_scan < 1 || current_scan > n_scans) {
      |                               ~~~~~~~~~~~~~^~~~~~~~~
RcppPwiz.cpp: In member function ‘Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)’:
RcppPwiz.cpp:853:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  853 |     } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {
      |                                      ~~~~~~~~~~~^~~~~~~~~~~~~
RcppPwiz.cpp:863:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pwiz::msdata::TimeIntensityPair>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  863 |       for (int i = 0; i < pairs.size(); i++) {
      |                       ~~^~~~~~~~~~~~~~
RcppPwiz.cpp: In member function ‘Rcpp::NumericMatrix RcppPwiz::get3DMap(std::vector<int>, double, double, double)’:
RcppPwiz.cpp:1014:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1014 |       for (int i = 0; i < scanNumbers.size(); i++)
      |                       ~~^~~~~~~~~~~~~~~~~~~~
RcppPwiz.cpp:1020:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pwiz::msdata::MZIntensityPair>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1020 |    for (int k=0; k < pairs.size(); k++)
      |                  ~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppPwizModule.cpp -o RcppPwizModule.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from RcppPwiz.h:12,
                 from RcppPwizModule.cpp:2:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from pwiz/data/msdata/Reader.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:30,
                 from RcppPwiz.h:12,
                 from RcppPwizModule.cpp:2:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppIdent.cpp -o RcppIdent.o
RcppIdent.cpp: In member function ‘Rcpp::DataFrame RcppIdent::getScore()’:
RcppIdent.cpp:293:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  293 |    for (size_t j = 0; j < nCvParams; j++) {
      |                       ~~^~~~~~~~~~~
RcppIdent.cpp: In member function ‘Rcpp::List RcppIdent::getPara()’:
RcppIdent.cpp:382:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pwiz::data::CVParam>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  382 |     for(int i = 0 ; i < sip[0]->additionalSearchParams.cvParams.size(); i++)
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RcppIdent.cpp:388:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pwiz::data::UserParam>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  388 |     for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++)
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppIdentModule.cpp -o RcppIdentModule.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
In file included from ./boost/checked_delete.hpp:15,
                 from ./boost/smart_ptr/detail/sp_counted_impl.hpp:27,
                 from ./boost/smart_ptr/detail/shared_count.hpp:27,
                 from ./boost/smart_ptr/shared_ptr.hpp:17,
                 from ./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/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = pwiz::data::MemoryIndex::Impl]’:
./boost/smart_ptr/detail/shared_count.hpp:154:34:   required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::MemoryIndex::Impl]’
./boost/smart_ptr/shared_ptr.hpp:279:20:   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/smart_ptr/shared_ptr.hpp:373:44:   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/core/checked_delete.hpp:36:5: warning: deleting object of polymorphic class type ‘pwiz::data::MemoryIndex::Impl’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
   36 |     delete x;
      |     ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
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]
  133 |     return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:135:40: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  135 |             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]
  136 |             key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from pwiz/data/common/cv.cpp:25029:
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 ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  102 |         for (int o=0;o<oboPrefixesSize_;++o)
      |                      ~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/checked_delete.hpp:15,
                 from ./boost/smart_ptr/detail/sp_counted_impl.hpp:27,
                 from ./boost/smart_ptr/detail/shared_count.hpp:27,
                 from ./boost/smart_ptr/shared_ptr.hpp:17,
                 from ./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/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = pwiz::data::BinaryIndexStream::Impl]’:
./boost/smart_ptr/detail/shared_count.hpp:154:34:   required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl]’
./boost/smart_ptr/shared_ptr.hpp:279:20:   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/smart_ptr/shared_ptr.hpp:373:44:   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:417:103:   required from here
./boost/core/checked_delete.hpp:36:5: warning: deleting object of polymorphic class type ‘pwiz::data::BinaryIndexStream::Impl’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
   36 |     delete x;
      |     ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o
In file included from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:29,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
                 from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o
In file included 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:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
                 from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o
In file included from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
                 from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:25:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o
In file included from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
                 from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o
In file included from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
                 from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:30,
                 from pwiz/data/msdata/DefaultReaderList.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:29:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from pwiz/data/msdata/Reader.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
In file included 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:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:27:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
                 from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.hpp:31,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:28:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:30,
                 from pwiz/data/msdata/Reader.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from pwiz/data/msdata/Reader.hpp:29,
                 from pwiz/data/msdata/Reader.cpp:26:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:27:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
                 from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
                 from pwiz/data/msdata/Serializer_mz5.hpp:32,
                 from pwiz/data/msdata/Serializer_mz5.cpp:28:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/SpectrumListBase.cpp -o pwiz/data/msdata/SpectrumListBase.o
In file included from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumListBase.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
In file included 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:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
In file included 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:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from ./boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from ./boost/smart_ptr/detail/yield_k.hpp:23,
                 from ./boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from ./boost/smart_ptr/detail/spinlock.hpp:42,
                 from ./boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from ./boost/smart_ptr/shared_ptr.hpp:29,
                 from ./boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:30,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/config/pragma_message.hpp:24:34: note: #pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
./boost/bind.hpp:36:1: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
In file included 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:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:27:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
                 from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.hpp:31,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:28:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
In file included from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
pwiz/data/msdata/BinaryDataEncoder.cpp: In member function ‘void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)’:
pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: ‘byteCount’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  302 |         filterArray<zlib_compressor>(byteBuffer, byteCount,compressed);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: ‘byteBuffer’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
pwiz/data/msdata/MSData.cpp: In member function ‘virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const string&, char) const’:
pwiz/data/msdata/MSData.cpp:1086:20: warning: control reaches end of non-void function [-Wreturn-type]
 1086 |     vector<string> abbreviatedTokens, actualTokens;
      |                    ^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
In file included 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:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
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=]
   84 |     } catch (index_not_found e){
      |                              ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
pwiz/data/msdata/IO.cpp: In function ‘void pwiz::msdata::IO::writeBinaryDataArray(pwiz::minimxml::XMLWriter&, const BinaryDataArrayType&, const pwiz::msdata::BinaryDataEncoder::Config&)’:
pwiz/data/msdata/IO.cpp:1657:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
 1657 |     if (usedConfig.byteOrder == BinaryDataEncoder::ByteOrder_BigEndian)
      |     ^~
pwiz/data/msdata/IO.cpp:1660:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 1660 |  bool zlib = false; // Handle numpress+zlib
      |  ^~~~
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:2132:35: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 2132 |             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:2836:31: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 2836 |         else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
      |                  ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
In file included 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:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
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]
  125 |     return (done() && &that.spectrumList_==&pastEndMarker_ ||
      |             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  127 |             &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]
  141 |     return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
      |            ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
In file included from pwiz/data/msdata/Reader.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:30,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  114 |     } else if (init == mask) {
      |                ~~~~~^~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
In file included from ./pwiz/data/msdata/MSData.hpp:29,
                 from ./pwiz/data/msdata/SpectrumWorkerThreads.hpp:26,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
In file included from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:36:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
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]
  478 |     bool strict;
      |          ^~~~~~
pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning:   ‘int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides’ [-Wreorder]
   85 |     int nPeptides;
      |         ^~~~~~~~~
pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning:   when initialized here [-Wreorder]
   91 |     Handler_protXML(IdentData& mzid,
      |     ^~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
In file included from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:33:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
pwiz/data/identdata/Serializer_pepXML.cpp: In member function ‘void pwiz::identdata::Serializer_pepXML::write(std::ostream&, const pwiz::identdata::IdentData&, const string&, const pwiz::util::IterationListenerRegistry*) const’:
pwiz/data/identdata/Serializer_pepXML.cpp:801:52: warning: ‘lastSpectrumIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  801 |             if (sii.chargeState != lastChargeState || spectrumIndex != lastSpectrumIndex)
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/identdata/Serializer_pepXML.cpp:775:26: note: ‘lastSpectrumIndex’ was declared here
  775 |     int lastChargeState, lastSpectrumIndex;
      |                          ^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
pwiz/data/identdata/References.cpp: In function ‘void pwiz::identdata::References::resolve(std::vector<boost::shared_ptr<pwiz::identdata::Contact> >&, pwiz::identdata::IdentData&)’:
pwiz/data/identdata/References.cpp:148:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
  148 |         else if (dynamic_cast<Person*>(c.get()))
      |                 ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
pwiz/data/proteome/Modification.cpp:89:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   89 |     auto_ptr<Formula> formula_;
      |     ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from ./boost/smart_ptr/detail/shared_count.hpp:27,
                 from ./boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
pwiz/utility/minimxml/SAXParser.cpp: In function ‘void pwiz::minimxml::SAXParser::parse(std::istream&, pwiz::minimxml::SAXParser::Handler&)’:
pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: ‘inCDATA’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  549 |                 if (inCDATA)
      |                 ^~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
pwiz/utility/misc/IntegerSet.cpp: In member function ‘bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const’:
pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  307 |     return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/misc/BinaryData.cpp -o pwiz/utility/misc/BinaryData.o
In file included from pwiz/utility/misc/BinaryData.cpp:24:
pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
  124 | #pragma region Ctors/Dtor
      | 
pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  136 | #pragma endregion
      | 
pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
  138 | #pragma region Iterators/accessors
      | 
pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  267 | #pragma endregion
      | 
pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
  269 | #pragma region Mutators
      | 
pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion  [-Wunknown-pragmas]
  377 | #pragma endregion
      | 
pwiz/utility/misc/BinaryData.cpp:302: warning: ignoring #pragma managed  [-Wunknown-pragmas]
  302 | #pragma managed(push, off)
      | 
pwiz/utility/misc/BinaryData.cpp:474: warning: ignoring #pragma managed  [-Wunknown-pragmas]
  474 | #pragma managed(pop)
      | 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwiz/utility/misc/String.cpp -o pwiz/utility/misc/String.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o mzR.so 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/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_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/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/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.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/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/BinaryData.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 ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o -lpthread /home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/library/00LOCK-mzR/00new/mzR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mzR)

Tests output

mzR.Rcheck/tests/runTests.Rout


R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library("mzR")
Loading required package: Rcpp
> library("msdata")
> 
> 
> ## Catch warnings as well:
> #options(warn = 2)
> 
> BiocGenerics:::testPackage("mzR")
Loading required namespace: XML
reading Tandem.mzid.gz... DONE!
Mass Spectrometry file handle.
Filename:  MM14.mzML 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  threonine_i2_e35_pH_tree.mzXML 
Number of scans:  55 
Unknown IO errorfailed to load external entity "http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_3.2.xsd"
Element '{http://www.w3.org/2001/XMLSchema}include': Failed to load the document 'http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_3.2.xsd' for inclusion.


RUNIT TEST PROTOCOL -- Fri Nov 25 22:14:17 2022 
*********************************************** 
Number of test functions: 29 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mzR RUnit Tests - 29 test functions, 0 errors, 0 failures
Number of test functions: 29 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: pwiz not yet initialized. 
2: pwiz not yet initialized. 
3: In XML::xmlTreeParse(system.file("extdata", "mzXML_idx_3.2.xsd.xml",  :
  NULL value for external reference
> 
> proc.time()
   user  system elapsed 
 30.399   1.225  31.868 

Example timings

mzR.Rcheck/mzR-Ex.timings

nameusersystemelapsed
copyWriteMSData0.1110.0040.109
isolationWindow-methods1.0630.1361.192
metadata0.1480.0090.161
mzR-class0.0290.0080.037
openMSfile0.0550.0040.059
peaks0.9300.0320.958
writeMSData0.0700.0000.066