############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf mzR.buildbin-libdir && mkdir mzR.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=mzR.buildbin-libdir mzR_2.29.3.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'mzR' ... ** using staged installation ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture 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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppPwiz.cpp -o RcppPwiz.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from RcppPwiz.h:12, from RcppPwiz.cpp:1: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/MSDataFile.hpp:29, from RcppPwiz.h:12, from RcppPwiz.cpp:1: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : 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, from RcppPwiz.h:12, from RcppPwiz.cpp:1: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RcppPwiz.cpp: In member function 'Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector)': RcppPwiz.cpp:406:44: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] if (current_scan < 1 || current_scan > n_scans) { ~~~~~~~~~~~~~^~~~~~~~~ RcppPwiz.cpp: In member function 'void RcppPwiz::addSpectrumList(pwiz::msdata::MSData&, Rcpp::DataFrame&, Rcpp::List&, bool)': RcppPwiz.cpp:774:29: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] if (precursorScanNum[i] > 0 | precursorMZ[i] > 0) { RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)': RcppPwiz.cpp:849:49: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) { ~~~~~~~~~~~^~~~~~~~~~~~~ RcppPwiz.cpp:859:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < pairs.size(); i++) { ~~^~~~~~~~~~~~~~ RcppPwiz.cpp: In member function 'Rcpp::NumericMatrix RcppPwiz::get3DMap(std::vector, double, double, double)': RcppPwiz.cpp:1010:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < scanNumbers.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~ RcppPwiz.cpp:1016:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int k=0; k < pairs.size(); k++) ~~^~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppPwizModule.cpp -o RcppPwizModule.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from RcppPwiz.h:12, from RcppPwizModule.cpp:2: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/MSDataFile.hpp:29, from RcppPwiz.h:12, from RcppPwizModule.cpp:2: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : 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, from RcppPwiz.h:12, from RcppPwizModule.cpp:2: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition RcppIdent.cpp: In member function 'Rcpp::DataFrame RcppIdent::getScore()': RcppIdent.cpp:293:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] for (size_t j = 0; j < nCvParams; j++) { ~~^~~~~~~~~~~ RcppIdent.cpp: In member function 'Rcpp::List RcppIdent::getPara()': RcppIdent.cpp:382:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i = 0 ; i < sip[0]->additionalSearchParams.cvParams.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RcppIdent.cpp:388:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::MemoryIndex::Impl]': ./boost/smart_ptr/detail/shared_count.hpp:154:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::MemoryIndex::Impl]' ./boost/smart_ptr/shared_ptr.hpp:279:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, boost::detail::shared_count&) [with T = pwiz::data::MemoryIndex::Impl; Y = pwiz::data::MemoryIndex::Impl]' ./boost/smart_ptr/shared_ptr.hpp:373:44: required from 'boost::shared_ptr::shared_ptr(Y*) [with Y = pwiz::data::MemoryIndex::Impl; T = pwiz::data::MemoryIndex::Impl]' pwiz/data/common/MemoryIndex.cpp:73:58: required from here ./boost/core/checked_delete.hpp:36:5: warning: deleting object of polymorphic class type 'pwiz::data::MemoryIndex::Impl' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete x; ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)': pwiz/data/common/CVTranslator.cpp:133:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses] return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ pwiz/data/common/CVTranslator.cpp:135:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ pwiz/data/common/CVTranslator.cpp:136:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from pwiz/data/common/cv.cpp:25029: pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)': pwiz/data/common/cv.inl:102:23: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] for (int o=0;o: note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::BinaryIndexStream::Impl]': ./boost/smart_ptr/detail/shared_count.hpp:154:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl]' ./boost/smart_ptr/shared_ptr.hpp:279:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, boost::detail::shared_count&) [with T = pwiz::data::BinaryIndexStream::Impl; Y = pwiz::data::BinaryIndexStream::Impl]' ./boost/smart_ptr/shared_ptr.hpp:373:44: required from 'boost::shared_ptr::shared_ptr(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl; T = pwiz::data::BinaryIndexStream::Impl]' pwiz/data/common/BinaryIndexStream.cpp:417:103: required from here ./boost/core/checked_delete.hpp:36:5: warning: deleting object of polymorphic class type 'pwiz::data::BinaryIndexStream::Impl' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete x; ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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/Configuration_mz5.cpp:24: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o In file included from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : 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, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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/mz5/ReferenceRead_mz5.cpp:24: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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/ReferenceWrite_mz5.cpp:24: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(pop) In file included from pwiz/data/msdata/Reader.hpp:29, from pwiz/data/msdata/DefaultReaderList.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o In file included from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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/Reader.cpp:26: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(pop) In file included from pwiz/data/msdata/Reader.hpp:29, from pwiz/data/msdata/Reader.cpp:26: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumListBase.cpp -o pwiz/data/msdata/SpectrumListBase.o In file included from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumListBase.cpp:25: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumListBase.cpp:25: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o In file included from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o In file included from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from pwiz/data/msdata/SpectrumList_mzML.cpp:31: ./boost/bind.hpp:41:1: note: #pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. ) ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o In file included from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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/SpectrumList_mz5.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:28: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o In file included from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : 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::__cxx11::string&, size_t*)': pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteCount' may be used uninitialized in this function [-Wmaybe-uninitialized] filterArray(byteBuffer, byteCount,compressed); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteBuffer' may be used uninitialized in this function [-Wmaybe-uninitialized] "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/MSData.cpp:25: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const string&, char) const': pwiz/data/msdata/MSData.cpp:1086:20: warning: control reaches end of non-void function [-Wreturn-type] vector abbreviatedTokens, actualTokens; ^~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o In file included from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition pwiz/data/msdata/SpectrumList_mzXML.cpp: In constructor 'pwiz::msdata::{anonymous}::SpectrumList_mzXMLImpl::SpectrumList_mzXMLImpl(boost::shared_ptr >, const pwiz::msdata::MSData&, bool)': pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=] } catch (index_not_found e){ ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : 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] if (usedConfig.byteOrder == BinaryDataEncoder::ByteOrder_BigEndian) ^~ pwiz/data/msdata/IO.cpp:1660:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' bool zlib = false; // Handle numpress+zlib ^~~~ pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': pwiz/data/msdata/IO.cpp:2132:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses] else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': pwiz/data/msdata/IO.cpp:2836:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o In file included from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : 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] return (done() && &that.spectrumList_==&pastEndMarker_ || ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses] &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::done() const': pwiz/data/msdata/SpectrumIterator.cpp:141:34: warning: suggest parentheses around '&&' within '||' [-Wparentheses] return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() || ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : 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, from pwiz/data/msdata/MSDataFile.cpp:26: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] } else if (init == mask) { ~~~~~^~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o In file included from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(pop) "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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 >*)': pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: 'pwiz::identdata::{anonymous}::Handler_protXML::strict' will be initialized after [-Wreorder] bool strict; ^~~~~~ pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning: 'int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides' [-Wreorder] int nPeptides; ^~~~~~~~~ pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning: when initialized here [-Wreorder] Handler_protXML(IdentData& mzid, ^~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor ./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors ./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators ./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion ./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) ./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) ./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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 string&, const pwiz::util::IterationListenerRegistry*)': pwiz/data/identdata/Serializer_pepXML.cpp:801:52: warning: 'lastSpectrumIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] if (sii.chargeState != lastChargeState || spectrumIndex != lastSpectrumIndex) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition pwiz/data/identdata/References.cpp: In function 'void pwiz::identdata::References::resolve(std::vector >&, pwiz::identdata::IdentData&)': pwiz/data/identdata/References.cpp:148:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] else if (dynamic_cast(c.get())) ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition pwiz/data/proteome/Modification.cpp:89:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr formula_; ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/smart_ptr/detail/sp_counted_impl.hpp:35, from ./boost/smart_ptr/detail/shared_count.hpp:27, from ./boost/smart_ptr/shared_ptr.hpp:17, from ./boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, pwiz::minimxml::SAXParser::Handler&)': pwiz/utility/minimxml/SAXParser.cpp:463:20: warning: offset '1' outside bounds of constant string [-Warray-bounds] PWIZ_API_DECL void parse(istream& is, Handler& handler) ^~~~~ pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: 'inCDATA' may be used uninitialized in this function [-Wmaybe-uninitialized] if (inCDATA) ^~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : 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] return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/misc/BinaryData.cpp -o pwiz/utility/misc/BinaryData.o In file included from pwiz/utility/misc/BinaryData.cpp:24: pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas] #pragma region Ctors/Dtor pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas] #pragma region Iterators/accessors pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas] #pragma region Mutators pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas] #pragma endregion pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(push) pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas] #pragma warning(disable: 4251) pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas] #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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition pwiz/utility/misc/BinaryData.cpp:302: warning: ignoring #pragma managed [-Wunknown-pragmas] #pragma managed(push, off) pwiz/utility/misc/BinaryData.cpp:474: warning: ignoring #pragma managed [-Wunknown-pragmas] #pragma managed(pop) "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition pwiz/utility/misc/Filesystem.cpp:29: warning: "_WIN32_WINNT" redefined #define _WIN32_WINNT 0x0600 In file included from C:/rtools40/mingw64/x86_64-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/wchar.h:9, from C:/rtools40/mingw64/include/c++/8.3.0/cwchar:44, from C:/rtools40/mingw64/include/c++/8.3.0/bits/postypes.h:40, from C:/rtools40/mingw64/include/c++/8.3.0/bits/char_traits.h:40, from C:/rtools40/mingw64/include/c++/8.3.0/string:40, from pwiz/utility/misc/String.hpp:27, from pwiz/utility/misc/Filesystem.hpp:34, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw64/x86_64-w64-mingw32/include/_mingw.h:225: note: this is the location of the previous definition #define _WIN32_WINNT 0x502 pwiz/utility/misc/Filesystem.cpp:31: warning: "NOMINMAX" redefined #define NOMINMAX In file included from C:/rtools40/mingw64/include/c++/8.3.0/x86_64-w64-mingw32/bits/c++config.h:508, from C:/rtools40/mingw64/include/c++/8.3.0/string:38, from pwiz/utility/misc/String.hpp:27, from pwiz/utility/misc/Filesystem.hpp:34, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/x86_64-w64-mingw32/bits/os_defines.h:45: note: this is the location of the previous definition #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] return GetProcAddress(GetModuleHandleA(LibraryName), ProcName); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/utility/misc/Filesystem.cpp: In function 'int {anonymous}::GetFileHandleTypeNumber(SYSTEM_HANDLE_INFORMATION*)': pwiz/utility/misc/Filesystem.cpp:156:106: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings] _NtQueryObject NtQueryObject = (_NtQueryObject)GetLibraryProcAddress("ntdll.dll", "NtQueryObject"); ^ pwiz/utility/misc/Filesystem.cpp:156:106: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings] pwiz/utility/misc/Filesystem.cpp:175:29: warning: comparison of integer expressions of different signedness: 'long int' and 'unsigned int' [-Wsign-compare] if (queryResult == STATUS_INFO_LENGTH_MISMATCH) ^ pwiz/utility/misc/Filesystem.cpp: In function 'bool pwiz::util::running_on_wine()': pwiz/utility/misc/Filesystem.cpp:238:65: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings] return GetLibraryProcAddress("ntdll.dll", "wine_get_version") != NULL; ^ pwiz/utility/misc/Filesystem.cpp:238:65: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings] pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::force_close_handles_to_filepath(const string&, bool)': pwiz/utility/misc/Filesystem.cpp:251:146: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings] _NtQuerySystemInformation NtQuerySystemInformation = (_NtQuerySystemInformation)GetLibraryProcAddress("ntdll.dll", "NtQuerySystemInformation"); ^ pwiz/utility/misc/Filesystem.cpp:251:146: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings] pwiz/utility/misc/Filesystem.cpp:262:112: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings] NtUnmapViewOfSection = (_NtUnmapViewOfSection)GetLibraryProcAddress("ntdll.dll", "NtUnmapViewOfSection"); ^ pwiz/utility/misc/Filesystem.cpp:262:112: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings] pwiz/utility/misc/Filesystem.cpp:269:106: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings] NtMapViewOfSection = (_NtMapViewOfSection)GetLibraryProcAddress("ntdll.dll", "NtMapViewOfSection"); ^ pwiz/utility/misc/Filesystem.cpp:269:106: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings] pwiz/utility/misc/Filesystem.cpp:286:20: warning: comparison of integer expressions of different signedness: 'NTSTATUS' {aka 'long int'} and 'unsigned int' [-Wsign-compare] 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] } while (status == STATUS_INFO_LENGTH_MISMATCH); ^ pwiz/utility/misc/Filesystem.cpp:372:59: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] if (!GetFileNameFromHandle((HANDLE)handleInfo.HandleValue, szPath, 260)) ^~~~~~~~~~~ pwiz/utility/misc/Filesystem.cpp:385:53: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] if (!CloseHandle((HANDLE)handleInfo.HandleValue)) ^~~~~~~~~~~ pwiz/utility/misc/Filesystem.cpp:397:69: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] NTSTATUS status = NtMapViewOfSection((HANDLE)handleInfo.HandleValue, currentProcessHandle, &viewBase, 0, 0, NULL, &viewSize, ViewShare, 0, PAGE_READONLY); ^~~~~~~~~~~ pwiz/utility/misc/Filesystem.cpp:413:49: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] if (!CloseHandle((HANDLE)handleInfo.HandleValue)) ^~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition boost_aux/libs/nowide/src/iostream.cpp: In member function 'virtual int boost::nowide::detail::console_input_buffer::underflow()': boost_aux/libs/nowide/src/iostream.cpp:189:13: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized] if(c==uf::incomplete) { ^~ boost_aux/libs/nowide/src/iostream.cpp:178:28: note: 'c' was declared here uf::code_point c; ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-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'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 #define _LARGEFILE_SOURCE : 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 # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition C:/rtools40/mingw64/bin/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 -LD:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -lws2_32 -lz -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/meat/mzR.buildbin-libdir/00LOCK-mzR/00new/mzR/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'mzR' finding HTML links ... done copyWriteMSData html isolationWindow-methods html metadata html mzR-class html finding level-2 HTML links ... done openMSfile html peaks html pwiz-version html writeMSData html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * MD5 sums packaged installation of 'mzR' as mzR_2.29.3.zip * DONE (mzR)