Multiple platform build/check report for BioC 3.21 - CHECK results for mzR on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4754
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4472
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4426
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4381
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4373
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 palomino7

To the developers/maintainers of the mzR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: mzR

Version: 2.41.1

Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mzR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings mzR_2.41.1.tar.gz

StartedAt: 2024-12-24 03:06:26 -0500 (Tue, 24 Dec 2024)

EndedAt: 2024-12-24 03:10:17 -0500 (Tue, 24 Dec 2024)

EllapsedTime: 231.5 seconds

RetCode: 0

Status: WARNINGS

CheckDir: mzR.Rcheck

Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mzR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings mzR_2.41.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/mzR.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'mzR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mzR' version '2.41.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'mzR' can be installed ... WARNING
Found the following significant warnings:
  RcppPwiz.cpp:408:56: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  RcppPwiz.cpp:854:55: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  ./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  pwiz/data/msdata/mz5/Datastructures_mz5.cpp:373:16: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 255 bytes from a string of length 255 [-Wstringop-truncation]
  pwiz/data/msdata/mz5/Datastructures_mz5.cpp:377:16: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  pwiz/data/msdata/mz5/Datastructures_mz5.cpp:381:16: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 63 bytes from a string of length 63 [-Wstringop-truncation]
  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: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  pwiz/utility/misc/Filesystem.cpp:156:78: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:156:91: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:238:34: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:238:47: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:251:107: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:251:120: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:262:77: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:262:90: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:269:73: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:269:86: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
See 'E:/biocbuild/bbs-3.21-bioc/meat/mzR.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mzR-class.Rd: Versioned-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
  -fpermissive
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/mzR/libs/x64/mzR.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 nor [v]sprintf. 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 4 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/mzR.Rcheck/00check.log'
for details.

Installation output

mzR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL mzR
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'mzR' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
using C++11
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/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./boost_aux/libs/nowide/src/iostream.o ./boost_aux/libs/nowide/src/cstdio.o ./boost_aux/libs/nowide/src/filebuf.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/Reader.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:30:
./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 long unsigned int'} [-Wsign-compare]
  407 |       if (current_scan < 1 || current_scan > n_scans) {
      |                               ~~~~~~~~~~~~~^~~~~~~~~
RcppPwiz.cpp:408:56: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  408 |         Rprintf("Index whichScan out of bounds [1 ... %d].\n", n_scans);
      |                                                       ~^       ~~~~~~~
      |                                                        |       |
      |                                                        int     size_t {aka long long unsigned int}
      |                                                       %lld
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 long unsigned int'} [-Wsign-compare]
  853 |     } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {
      |                                      ~~~~~~~~~~~^~~~~~~~~~~~~
RcppPwiz.cpp:854:55: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  854 |       Rprintf("Index whichChrom out of bounds [0 ... %d].\n", (clp->size())-1);
      |                                                      ~^       ~~~~~~~~~~~~~~~
      |                                                       |                    |
      |                                                       int                  size_t {aka long long unsigned int}
      |                                                      %lld
RcppPwiz.cpp:863:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::msdata::TimeIntensityPair>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  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 long unsigned int'} [-Wsign-compare]
 1014 |       for (int i = 0; i < scanNumbers.size(); i++)
      |                       ~~^~~~~~~~~~~~~~~~~~~~
RcppPwiz.cpp:1020:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::msdata::MZIntensityPair>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 1020 |           for (int k=0; k < pairs.size(); k++)
      |                         ~~^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/Reader.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:30:
./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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c RcppIdent.cpp -o RcppIdent.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 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/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
RcppIdent.cpp: In member function 'Rcpp::DataFrame RcppIdent::getScore()':
RcppIdent.cpp:293:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long 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 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 long unsigned int'} [-Wsign-compare]
  388 |     for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++)
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c RcppIdentModule.cpp -o RcppIdentModule.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 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/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
In file included from ./boost/config.hpp:57,
                 from ./boost/system/config.hpp:13,
                 from boost/libs/system/src/error_code.cpp:17:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
In file included from ./boost/config.hpp:57,
                 from boost/libs/regex/src/posix_api.cpp:21:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
In file included from ./boost/config.hpp:57,
                 from ./boost/regex/config.hpp:76,
                 from boost/libs/regex/src/regex_debug.cpp:22:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
In file included from ./boost/config.hpp:57,
                 from ./boost/regex/config.hpp:76,
                 from boost/libs/regex/src/regex.cpp:22:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o
In file included from ./boost/config.hpp:57,
                 from ./boost/regex/config.hpp:76,
                 from boost/libs/regex/src/wide_posix_api.cpp:21:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
In file included from ./boost/config.hpp:57,
                 from ./boost/regex/config.hpp:76,
                 from boost/libs/regex/src/static_mutex.cpp:20:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
In file included from ./boost/config.hpp:57,
                 from ./boost/exception/exception.hpp:9,
                 from ./boost/throw_exception.hpp:23,
                 from boost/libs/iostreams/src/zlib.cpp:17:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
In file included from ./boost/config.hpp:57,
                 from boost/libs/iostreams/src/file_descriptor.cpp:16:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
In file included from ./boost/config.hpp:57,
                 from ./boost/winapi/config.hpp:235,
                 from boost/libs/filesystem/src/platform_config.hpp:74,
                 from boost/libs/filesystem/src/operations.cpp:14:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
In file included from ./boost/config.hpp:57,
                 from ./boost/winapi/config.hpp:235,
                 from boost/libs/filesystem/src/platform_config.hpp:74,
                 from boost/libs/filesystem/src/directory.cpp:14:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
In file included from ./boost/config.hpp:57,
                 from ./boost/winapi/config.hpp:235,
                 from boost/libs/filesystem/src/platform_config.hpp:74,
                 from boost/libs/filesystem/src/exception.cpp:11:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
In file included from ./boost/config.hpp:57,
                 from ./boost/winapi/config.hpp:235,
                 from boost/libs/filesystem/src/platform_config.hpp:74,
                 from boost/libs/filesystem/src/path.cpp:10:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
In file included from ./boost/config.hpp:57,
                 from ./boost/winapi/config.hpp:235,
                 from boost/libs/filesystem/src/platform_config.hpp:74,
                 from boost/libs/filesystem/src/unique_path.cpp:13:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
In file included from ./boost/config.hpp:57,
                 from ./boost/winapi/config.hpp:235,
                 from boost/libs/filesystem/src/platform_config.hpp:74,
                 from boost/libs/filesystem/src/utf8_codecvt_facet.cpp:6:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
In file included from ./boost/config.hpp:57,
                 from ./boost/chrono/config.hpp:15,
                 from ./boost/chrono/duration.hpp:33,
                 from ./boost/chrono/chrono.hpp:11,
                 from ./boost/chrono/detail/inlined/chrono.hpp:13,
                 from boost/libs/chrono/src/chrono.cpp:14:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
In file included from ./boost/config.hpp:57,
                 from ./boost/chrono/config.hpp:15,
                 from ./boost/chrono/detail/inlined/process_cpu_clocks.hpp:15,
                 from boost/libs/chrono/src/process_cpu_clocks.cpp:17:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
In file included from ./boost/config.hpp:57,
                 from ./boost/chrono/config.hpp:15,
                 from ./boost/chrono/detail/inlined/thread_clock.hpp:14,
                 from boost/libs/chrono/src/thread_clock.cpp:18:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
In file included from ./boost/config.hpp:57,
                 from ./boost/iostreams/positioning.hpp:18,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
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:
./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*, 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:73:44:   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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 from ./boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)':
pwiz/data/common/CVTranslator.cpp:145:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  145 |     return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:147:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  147 |             key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:148:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  148 |             key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/common/cv.cpp:34:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/common/cv.cpp:26876:
pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)':
pwiz/data/common/cv.inl:103:23: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
  103 |         for (int o=0;o<oboPrefixesSize_;++o)
      |                      ~^~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/config.hpp:57,
                 from ./boost/iostreams/positioning.hpp:18,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from ./boost/thread/detail/thread.hpp:41,
                 from ./boost/thread/thread_only.hpp:22,
                 from ./boost/thread/thread.hpp:12,
                 from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\string:49,
                 from pwiz/data/common/Index.hpp:27:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
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:
./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*, 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:417:82:   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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 from ./boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:29:
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
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:
./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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o
In file included from 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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
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:
./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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:29:
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
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;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void pwiz::msdata::mz5::UserParamMZ5::init(const char*, const char*, const char*, long unsigned int)',
    inlined from 'pwiz::msdata::mz5::UserParamMZ5::UserParamMZ5(const pwiz::msdata::mz5::UserParamMZ5&)' at pwiz/data/msdata/mz5/Datastructures_mz5.cpp:345:9:
pwiz/data/msdata/mz5/Datastructures_mz5.cpp:373:16: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 255 bytes from a string of length 255 [-Wstringop-truncation]
  373 |         strncpy(this->name, name, USRNL);
      |         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/mz5/Datastructures_mz5.cpp:377:16: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  377 |         strncpy(this->value, value, USRVL);
      |         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/mz5/Datastructures_mz5.cpp:381:16: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 63 bytes from a string of length 63 [-Wstringop-truncation]
  381 |         strncpy(this->type, type, USRTL);
      |         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:29:
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
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:
./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;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/mz5/../SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/mz5/../SpectrumList_mz5.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:27:
./boost/container_hash/hash.hpp: At global scope:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\string:49,
                 from pwiz/data/msdata/mz5/../../common/cv.hpp:35,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:27:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:29:
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
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:
./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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from pwiz/data/msdata/Reader.hpp: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;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:30:
./boost/container_hash/hash.hpp: At global scope:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\string:49,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from ./pwiz/utility/misc/Std.hpp:28:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
In file included from ./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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
In file included from 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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:28:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\refwrap.h:39,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
In file included from 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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:29:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\refwrap.h:39,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 from ./boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/IterationListener.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:30:
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from pwiz/data/msdata/Reader.hpp: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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
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;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_mz5.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:29:
./boost/container_hash/hash.hpp: At global scope:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\string:49,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from ./pwiz/utility/misc/Std.hpp:28:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
In file included from 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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/Serializer_MGF.cpp:26:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\refwrap.h:39,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
In file included from 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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:26:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\refwrap.h:39,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\refwrap.h:39,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
In file included from ./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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\refwrap.h:39,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
In file included from ./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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\refwrap.h:39,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
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:
./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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
In file included from ./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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\refwrap.h:39,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_mz5.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:28:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\string:49,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from ./pwiz/utility/misc/Std.hpp:28:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
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:
./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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 from ./boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
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 [-Wmaybe-uninitialized]
  302 |         filterArray<zlib_compressor>(byteBuffer, byteCount,compressed);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/BinaryDataEncoder.cpp:131:12: note: 'byteCount' was declared here
  131 |     size_t byteCount;
      |            ^~~~~~~~~
pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteBuffer' may be used uninitialized [-Wmaybe-uninitialized]
  302 |         filterArray<zlib_compressor>(byteBuffer, byteCount,compressed);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: 'byteBuffer' was declared here
  132 |     const void* byteBuffer;
      |                 ^~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
In file included from ./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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\refwrap.h:39,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
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:1660:9: 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 std::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 std::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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
In file included from ./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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\refwrap.h:39,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/Reader.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:30:
./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;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:31:
./boost/container_hash/hash.hpp: At global scope:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\refwrap.h:39,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)':
pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  114 |     } else if (init == mask) {
      |                ~~~~~^~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from ./boost/multi_index/detail/hash_index_args.hpp:17,
                 from ./boost/multi_index/hashed_index_fwd.hpp:16,
                 from ./boost/multi_index/hashed_index.hpp:43,
                 from ./pwiz/utility/misc/mru_list.hpp:26,
                 from pwiz/data/msdata/MemoryMRUCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.hpp:28:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\refwrap.h:39,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
In file included from 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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:30:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/functional/hash.hpp:6,
                 from ./pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from ./pwiz/data/msdata/SpectrumListWrapper.hpp:28,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:27:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\string:49,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from ./pwiz/utility/misc/Std.hpp:28:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 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/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 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/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 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/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:36:
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 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/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:33:
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
pwiz/data/identdata/Serializer_pepXML.cpp: In function 'void pwiz::identdata::{anonymous}::write_spectrum_queries(pwiz::minimxml::XMLWriter&, const pwiz::identdata::IdentData&, const std::string&, const pwiz::util::IterationListenerRegistry*)':
pwiz/data/identdata/Serializer_pepXML.cpp:801:52: warning: 'lastSpectrumIndex' may be used uninitialized [-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 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/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 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/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 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/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 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:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
pwiz/data/proteome/Modification.cpp:89:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   89 |     auto_ptr<Formula> formula_;
      |     ^~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\memory:78,
                 from ./boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from ./boost/smart_ptr/detail/shared_count.hpp:27:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 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/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 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/Peptide.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, Handler&)':
pwiz/utility/minimxml/SAXParser.cpp:543:61: warning: offset '1' outside bounds of constant string [-Warray-bounds=]
  543 |                 Handler::Status status = wrangler.endElement(buffer.c_str()+1, position);
      |                                          ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: 'inCDATA' may be used uninitialized [-Wmaybe-uninitialized]
  549 |                 if (inCDATA)
      |                 ^~
pwiz/utility/minimxml/SAXParser.cpp:501:14: note: 'inCDATA' was declared here
  501 |         bool inCDATA;
      |              ^~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 from ./boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 from ./boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/Base64.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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:389: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  389 | #pragma warning(push)
      | 
pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  390 | #pragma warning(disable: 4251)
      | 
pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
  392 | #pragma warning(pop)
      | 
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from pwiz/utility/misc/BinaryData.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
pwiz/utility/misc/BinaryData.cpp:303: warning: ignoring '#pragma managed ' [-Wunknown-pragmas]
  303 | #pragma managed(push, off)
      | 
pwiz/utility/misc/BinaryData.cpp:475: warning: ignoring '#pragma managed ' [-Wunknown-pragmas]
  475 | #pragma managed(pop)
      | 
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
In file included from ./boost/config.hpp:57,
                 from ./boost/lexical_cast.hpp:21,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from pwiz/utility/misc/Std.hpp:29,
                 from pwiz/utility/misc/IterationListener.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 from ./boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
In file included from ./boost/config.hpp:57,
                 from ./boost/algorithm/string/std_containers_traits.hpp:18,
                 from ./boost/algorithm/string.hpp:18,
                 from pwiz/utility/misc/String.hpp:31,
                 from pwiz/utility/misc/Filesystem.hpp:34,
                 from pwiz/utility/misc/Filesystem.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
pwiz/utility/misc/Filesystem.cpp:29: warning: "_WIN32_WINNT" redefined
   29 |     #define _WIN32_WINNT 0x0600
      | 
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\include\corecrt.h:10,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\include\wchar.h:9,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\cwchar:44,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\postypes.h:40,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\char_traits.h:42,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\string:42,
                 from pwiz/utility/misc/String.hpp:27:
c:\rtools44\x86_64-w64-mingw32.static.posix\include\_mingw.h:232: note: this is the location of the previous definition
  232 | #define _WIN32_WINNT 0x0601
      | 
pwiz/utility/misc/Filesystem.cpp:31: warning: "NOMINMAX" redefined
   31 |     #define NOMINMAX
      | 
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\x86_64-w64-mingw32.static.posix\bits\c++config.h:679,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\requires_hosted.h:31,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\string:38:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\x86_64-w64-mingw32.static.posix\bits\os_defines.h:45: note: this is the location of the previous definition
   45 | #define NOMINMAX 1
      | 
pwiz/utility/misc/Filesystem.cpp: In function 'void* {anonymous}::GetLibraryProcAddress(PSTR, PSTR)':
pwiz/utility/misc/Filesystem.cpp:141:30: warning: invalid conversion from 'FARPROC' {aka 'long long int (*)()'} to 'PVOID' {aka 'void*'} [-fpermissive]
  141 |         return GetProcAddress(GetModuleHandleA(LibraryName), ProcName);
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              FARPROC {aka long long int (*)()}
pwiz/utility/misc/Filesystem.cpp: In function 'int {anonymous}::GetFileHandleTypeNumber(SYSTEM_HANDLE_INFORMATION*)':
pwiz/utility/misc/Filesystem.cpp:156:78: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  156 |         _NtQueryObject NtQueryObject = (_NtQueryObject)GetLibraryProcAddress("ntdll.dll", "NtQueryObject");
      |                                                                              ^~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:156:91: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  156 |         _NtQueryObject NtQueryObject = (_NtQueryObject)GetLibraryProcAddress("ntdll.dll", "NtQueryObject");
      |                                                                                           ^~~~~~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:175:29: warning: comparison of integer expressions of different signedness: 'long int' and 'unsigned int' [-Wsign-compare]
  175 |             if (queryResult == STATUS_INFO_LENGTH_MISMATCH)
      |                             ^
pwiz/utility/misc/Filesystem.cpp: In function 'bool pwiz::util::running_on_wine()':
pwiz/utility/misc/Filesystem.cpp:238:34: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  238 |     return GetLibraryProcAddress("ntdll.dll", "wine_get_version") != NULL;
      |                                  ^~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:238:47: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  238 |     return GetLibraryProcAddress("ntdll.dll", "wine_get_version") != NULL;
      |                                               ^~~~~~~~~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::force_close_handles_to_filepath(const std::string&, bool)':
pwiz/utility/misc/Filesystem.cpp:251:107: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  251 |     _NtQuerySystemInformation NtQuerySystemInformation = (_NtQuerySystemInformation)GetLibraryProcAddress("ntdll.dll", "NtQuerySystemInformation");
      |                                                                                                           ^~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:251:120: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  251 |     _NtQuerySystemInformation NtQuerySystemInformation = (_NtQuerySystemInformation)GetLibraryProcAddress("ntdll.dll", "NtQuerySystemInformation");
      |                                                                                                                        ^~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:262:77: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  262 |         NtUnmapViewOfSection = (_NtUnmapViewOfSection)GetLibraryProcAddress("ntdll.dll", "NtUnmapViewOfSection");
      |                                                                             ^~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:262:90: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  262 |         NtUnmapViewOfSection = (_NtUnmapViewOfSection)GetLibraryProcAddress("ntdll.dll", "NtUnmapViewOfSection");
      |                                                                                          ^~~~~~~~~~~~~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:269:73: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  269 |         NtMapViewOfSection = (_NtMapViewOfSection)GetLibraryProcAddress("ntdll.dll", "NtMapViewOfSection");
      |                                                                         ^~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:269:86: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  269 |         NtMapViewOfSection = (_NtMapViewOfSection)GetLibraryProcAddress("ntdll.dll", "NtMapViewOfSection");
      |                                                                                      ^~~~~~~~~~~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:286:20: warning: comparison of integer expressions of different signedness: 'NTSTATUS' {aka 'long int'} and 'unsigned int' [-Wsign-compare]
  286 |         if (status == STATUS_INFO_LENGTH_MISMATCH)
      |                    ^
pwiz/utility/misc/Filesystem.cpp:294:21: warning: comparison of integer expressions of different signedness: 'NTSTATUS' {aka 'long int'} and 'unsigned int' [-Wsign-compare]
  294 |     } while (status == STATUS_INFO_LENGTH_MISMATCH);
      |                     ^
pwiz/utility/misc/Filesystem.cpp:372:40: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  372 |             if (!GetFileNameFromHandle((HANDLE)handleInfo.HandleValue, szPath, 260))
      |                                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:385:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  385 |                 if (!CloseHandle((HANDLE)handleInfo.HandleValue))
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:397:50: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  397 |             NTSTATUS status = NtMapViewOfSection((HANDLE)handleInfo.HandleValue, currentProcessHandle, &viewBase, 0, 0, NULL, &viewSize, ViewShare, 0, PAGE_READONLY);
      |                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:413:30: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  413 |             if (!CloseHandle((HANDLE)handleInfo.HandleValue))
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 from ./boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from ./boost/config.hpp:57,
                 from ./boost/iostreams/positioning.hpp:18,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from ./boost/thread/detail/thread.hpp:41,
                 from ./boost/thread/thread_only.hpp:22,
                 from ./boost/thread/thread.hpp:12,
                 from ./boost/thread.hpp:13,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:77:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\string:49,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\locale_classes.h:40,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\locale:41,
                 from ./boost/iostreams/detail/config/codecvt.hpp:63,
                 from ./boost/iostreams/positioning.hpp:21:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
In file included from ./boost/config.hpp:57,
                 from ./boost/static_assert.hpp:17,
                 from pwiz/utility/misc/endian.hpp:28,
                 from pwiz/utility/misc/SHA1.cpp:10:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
In file included from ./boost/config.hpp:57,
                 from ./boost/static_assert.hpp:17,
                 from pwiz/utility/misc/endian.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
In file included from ./boost/config.hpp:57,
                 from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
                 from ./boost/smart_ptr/detail/shared_count.hpp:25,
                 from ./boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c pwiz/utility/misc/String.cpp -o pwiz/utility/misc/String.o
In file included from ./boost/config.hpp:57,
                 from ./boost/algorithm/string/std_containers_traits.hpp:18,
                 from ./boost/algorithm/string.hpp:18,
                 from pwiz/utility/misc/String.hpp:31,
                 from pwiz/utility/misc/String.cpp:21:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
In file included from ./boost/config.hpp:57,
                 from ./boost/winapi/config.hpp:235,
                 from boost/libs/filesystem/src/platform_config.hpp:74,
                 from boost/libs/filesystem/src/path_traits.cpp:12:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
In file included from ./boost/config.hpp:57,
                 from ./boost/winapi/config.hpp:235,
                 from boost/libs/filesystem/src/platform_config.hpp:74,
                 from boost/libs/filesystem/src/windows_file_codecvt.cpp:12:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
In file included from ./boost/config.hpp:57,
                 from ./boost/winapi/config.hpp:235,
                 from boost/libs/filesystem/src/platform_config.hpp:74,
                 from boost/libs/filesystem/src/codecvt_error_category.cpp:12:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/thread/src/win32/tss_pe.cpp -o boost/libs/thread/src/win32/tss_pe.o
In file included from ./boost/config.hpp:57,
                 from ./boost/winapi/config.hpp:235,
                 from boost/libs/thread/src/win32/tss_pe.cpp:10:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/thread/src/win32/tss_dll.cpp -o boost/libs/thread/src/win32/tss_dll.o
In file included from ./boost/config.hpp:57,
                 from ./boost/winapi/config.hpp:235,
                 from boost/libs/thread/src/win32/tss_dll.cpp:6:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost/libs/thread/src/win32/thread.cpp -o boost/libs/thread/src/win32/thread.o
In file included from ./boost/config.hpp:57,
                 from ./boost/winapi/config.hpp:235,
                 from boost/libs/thread/src/win32/thread.cpp:10:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/functional/hash.hpp:6,
                 from ./boost/thread/detail/thread.hpp:41,
                 from ./boost/thread/thread_only.hpp:22,
                 from boost/libs/thread/src/win32/thread.cpp:11:
./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\string:49,
                 from ./boost/date_time/c_time.hpp:18,
                 from ./boost/date_time/time_clock.hpp:16,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/win32/thread_data.hpp:10,
                 from ./boost/thread/thread_only.hpp:15:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost_aux/libs/nowide/src/iostream.cpp -o boost_aux/libs/nowide/src/iostream.o
In file included from ./boost/config.hpp:57,
                 from ./boost/nowide/config.hpp:14,
                 from ./boost/nowide/iostream.hpp:12,
                 from boost_aux/libs/nowide/src/iostream.cpp:9:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
boost_aux/libs/nowide/src/iostream.cpp:225:5: warning: default argument given for parameter 1 of 'boost::nowide::detail::winconsole_istream::winconsole_istream(boost::nowide::detail::winconsole_ostream*)' [-fpermissive]
  225 |     winconsole_istream::winconsole_istream(winconsole_ostream* tieStream=0) : std::istream(0)
      |     ^~~~~~~~~~~~~~~~~~
./boost/nowide/iostream.hpp:55:22: note: previous specification in 'boost::nowide::detail::winconsole_istream::winconsole_istream(boost::nowide::detail::winconsole_ostream*)' here
   55 |             explicit winconsole_istream(winconsole_ostream* tieStream=0);
      |                      ^~~~~~~~~~~~~~~~~~
boost_aux/libs/nowide/src/iostream.cpp: In member function 'size_t boost::nowide::detail::console_input_buffer::read()':
boost_aux/libs/nowide/src/iostream.cpp:185:13: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized]
  185 |             if(c==uf::illegal)
      |             ^~
boost_aux/libs/nowide/src/iostream.cpp:178:28: note: 'c' was declared here
  178 |             uf::code_point c;
      |                            ^
In member function 'int boost::nowide::detail::console_output_buffer::write(const char*, int)',
    inlined from 'virtual int boost::nowide::detail::console_output_buffer::overflow(int)' at boost_aux/libs/nowide/src/iostream.cpp:49:33:
boost_aux/libs/nowide/src/iostream.cpp:82:13: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized]
   82 |             if(c==uf::illegal)
      |             ^~
boost_aux/libs/nowide/src/iostream.cpp: In member function 'virtual int boost::nowide::detail::console_output_buffer::overflow(int)':
boost_aux/libs/nowide/src/iostream.cpp:76:28: note: 'c' was declared here
   76 |             uf::code_point c;
      |                            ^
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost_aux/libs/nowide/src/cstdio.cpp -o boost_aux/libs/nowide/src/cstdio.o
In file included from ./boost/config.hpp:57,
                 from ./boost/nowide/config.hpp:14,
                 from ./boost/nowide/cstdio.hpp:12,
                 from boost_aux/libs/nowide/src/cstdio.cpp:19:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG   -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c boost_aux/libs/nowide/src/filebuf.cpp -o boost_aux/libs/nowide/src/filebuf.o
boost_aux/libs/nowide/src/filebuf.cpp:23: warning: "_LARGEFILE_SOURCE" redefined
   23 | #define _LARGEFILE_SOURCE
      | 
<command-line>: note: this is the location of the previous definition
In file included from ./boost/config.hpp:57,
                 from ./boost/nowide/config.hpp:14,
                 from ./boost/nowide/filebuf.hpp:12,
                 from boost_aux/libs/nowide/src/filebuf.cpp:34:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
   61 | #  define BOOST_HAS_WINTHREADS
      | 
<command-line>: note: this is the location of the previous definition
g++ -shared -s -static-libgcc -o mzR.dll tmp.def 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/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./boost_aux/libs/nowide/src/iostream.o ./boost_aux/libs/nowide/src/cstdio.o ./boost_aux/libs/nowide/src/filebuf.o -lpthread -LE:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -lws2_32 -lz -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-mzR/00new/mzR/libs/x64
** 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
** 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


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'citation()' on how to cite R or R packages in publications.

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'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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 -- Tue Dec 24 03:10:08 2024 
*********************************************** 
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 
  33.50    3.98   40.56

Example timings

mzR.Rcheck/mzR-Ex.timings

name	user	system	elapsed
copyWriteMSData	0.14	0.00	0.15
isolationWindow-methods	1.24	0.41	1.67
metadata	0.92	0.69	1.65
mzR-class	0.03	0.01	0.11
openMSfile	0.94	0.50	1.44
peaks	0.95	0.08	1.04
writeMSData	0.11	0.00	0.11