############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf mzR.buildbin-libdir && mkdir mzR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mzR_2.39.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mzR.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=mzR.buildbin-libdir mzR_2.39.0.tar.gz' >>>>>>> * installing *source* package ‘mzR’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ rm -f RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppPwiz.cpp -o RcppPwiz.o In file included from RcppPwiz.cpp:1: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:30: In file included from ./pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) RcppPwiz.cpp:408:57: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Index whichScan out of bounds [1 ... %d].\n", n_scans); ~~ ^~~~~~~ %zu RcppPwiz.cpp:854:63: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Index whichChrom out of bounds [0 ... %d].\n", (clp->size())-1); ~~ ^~~~~~~~~~~~~~~ %lu 3 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppPwizModule.cpp -o RcppPwizModule.o In file included from RcppPwizModule.cpp:2: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:30: In file included from ./pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppIdent.cpp -o RcppIdent.o In file included from RcppIdent.cpp:1: In file included from ./RcppIdent.h:11: In file included from ./pwiz/data/identdata/IdentDataFile.hpp:29: In file included from ./pwiz/data/identdata/IdentData.hpp:30: In file included from ./pwiz/data/proteome/Digestion.hpp:32: In file included from ./pwiz/data/proteome/Peptide.hpp:183: ./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppIdentModule.cpp -o RcppIdentModule.o In file included from RcppIdentModule.cpp:2: In file included from ./RcppIdent.h:11: In file included from ./pwiz/data/identdata/IdentDataFile.hpp:29: In file included from ./pwiz/data/identdata/IdentData.hpp:30: In file included from ./pwiz/data/proteome/Digestion.hpp:32: In file included from ./pwiz/data/proteome/Peptide.hpp:183: ./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o In file included from pwiz/data/common/MemoryIndex.cpp:25: In file included from pwiz/data/common/MemoryIndex.hpp:26: In file included from pwiz/data/common/Index.hpp:30: In file included from ./boost/shared_ptr.hpp:17: In file included from ./boost/smart_ptr/shared_ptr.hpp:17: In file included from ./boost/smart_ptr/detail/shared_count.hpp:27: In file included from ./boost/smart_ptr/detail/sp_counted_impl.hpp:27: In file included from ./boost/checked_delete.hpp:15: ./boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'pwiz::data::MemoryIndex::Impl' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ ./boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ ./boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ ./boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ pwiz/data/common/MemoryIndex.cpp:73:44: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here PWIZ_API_DECL MemoryIndex::MemoryIndex() : impl_(new Impl) {} ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o pwiz/data/common/CVTranslator.cpp:145:53: warning: '&&' within '||' [-Wlogical-op-parentheses] return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ ~~ pwiz/data/common/CVTranslator.cpp:145:53: note: place parentheses around the '&&' expression to silence this warning return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || ^ ( ) pwiz/data/common/CVTranslator.cpp:146:40: warning: '&&' within '||' [-Wlogical-op-parentheses] key=="pi_" && value==MS_PI && cvid==UO_pi || // MS_PI==photoionization, UO_pi==3.14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ pwiz/data/common/CVTranslator.cpp:146:40: note: place parentheses around the '&&' expression to silence this warning key=="pi_" && value==MS_PI && cvid==UO_pi || // MS_PI==photoionization, UO_pi==3.14 ^ ( ) pwiz/data/common/CVTranslator.cpp:147:40: warning: '&&' within '||' [-Wlogical-op-parentheses] key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ pwiz/data/common/CVTranslator.cpp:147:40: note: place parentheses around the '&&' expression to silence this warning key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point ^ ( ) pwiz/data/common/CVTranslator.cpp:148:40: warning: '&&' within '||' [-Wlogical-op-parentheses] key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ pwiz/data/common/CVTranslator.cpp:148:40: note: place parentheses around the '&&' expression to silence this warning key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 ^ ( ) 4 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o In file included from pwiz/data/common/BinaryIndexStream.cpp:25: In file included from pwiz/data/common/BinaryIndexStream.hpp:26: In file included from pwiz/data/common/Index.hpp:30: In file included from ./boost/shared_ptr.hpp:17: In file included from ./boost/smart_ptr/shared_ptr.hpp:17: In file included from ./boost/smart_ptr/detail/shared_count.hpp:27: In file included from ./boost/smart_ptr/detail/sp_counted_impl.hpp:27: In file included from ./boost/checked_delete.hpp:15: ./boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'pwiz::data::BinaryIndexStream::Impl' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ ./boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ ./boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ ./boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ pwiz/data/common/BinaryIndexStream.cpp:417:82: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here PWIZ_API_DECL BinaryIndexStream::BinaryIndexStream(shared_ptr isPtr) : impl_(new Impl(isPtr)) {} ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o In file included from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o In file included from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o In file included from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:25: In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o In file included from pwiz/data/msdata/DefaultReaderList.cpp:29: In file included from pwiz/data/msdata/DefaultReaderList.hpp:29: In file included from pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o In file included from pwiz/data/msdata/ChromatogramList_mz5.cpp:28: In file included from pwiz/data/msdata/ChromatogramList_mz5.hpp:31: In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o pwiz/data/msdata/Serializer_MSn.cpp:44:11: warning: unused variable 'sizeChargeMSn' [-Wunused-const-variable] const int sizeChargeMSn = 12; // struct Charge{ int z; double mass; } ^ pwiz/data/msdata/Serializer_MSn.cpp:45:11: warning: unused variable 'sizePeakMSn' [-Wunused-const-variable] const int sizePeakMSn = 12; // struct Peak{ double mz; float intensity; } ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o In file included from pwiz/data/msdata/Reader.cpp:26: In file included from pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o In file included from pwiz/data/msdata/Serializer_mz5.cpp:28: In file included from pwiz/data/msdata/Serializer_mz5.hpp:32: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumListBase.cpp -o pwiz/data/msdata/SpectrumListBase.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o In file included from pwiz/data/msdata/SpectrumList_mzML.cpp:31: ./boost/bind.hpp:36:1: warning: 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. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ ./boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :43:2: note: expanded from here 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.") ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.o In file included from pwiz/data/msdata/SpectrumList_mz5.cpp:28: In file included from pwiz/data/msdata/SpectrumList_mz5.hpp:31: In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o pwiz/data/msdata/MSData.cpp:1115:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o pwiz/data/msdata/IO.cpp:2132:35: warning: '&&' within '||' [-Wlogical-op-parentheses] else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ pwiz/data/msdata/IO.cpp:2132:35: note: place parentheses around the '&&' expression to silence this warning else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") ^ ( ) pwiz/data/msdata/IO.cpp:2836:31: warning: '&&' within '||' [-Wlogical-op-parentheses] else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ pwiz/data/msdata/IO.cpp:2836:31: note: place parentheses around the '&&' expression to silence this warning else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || ^ ( ) 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o pwiz/data/msdata/SpectrumList_BTDX.cpp:279:19: warning: private field 'msd_' is not used [-Wunused-private-field] const MSData& msd_; ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o pwiz/data/msdata/SpectrumIterator.cpp:125:20: warning: '&&' within '||' [-Wlogical-op-parentheses] return (done() && &that.spectrumList_==&pastEndMarker_ || ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ pwiz/data/msdata/SpectrumIterator.cpp:125:20: note: place parentheses around the '&&' expression to silence this warning return (done() && &that.spectrumList_==&pastEndMarker_ || ^ ( ) pwiz/data/msdata/SpectrumIterator.cpp:126:45: warning: '&&' within '||' [-Wlogical-op-parentheses] &spectrumList_==&pastEndMarker_ && that.done() || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ pwiz/data/msdata/SpectrumIterator.cpp:126:45: note: place parentheses around the '&&' expression to silence this warning &spectrumList_==&pastEndMarker_ && that.done() || ^ ( ) pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: '&&' within '||' [-Wlogical-op-parentheses] &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/SpectrumIterator.cpp:127:49: note: place parentheses around the '&&' expression to silence this warning &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_); ^ ( ) pwiz/data/msdata/SpectrumIterator.cpp:141:34: warning: '&&' within '||' [-Wlogical-op-parentheses] return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() || ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ pwiz/data/msdata/SpectrumIterator.cpp:141:34: note: place parentheses around the '&&' expression to silence this warning return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() || ^ ( ) 4 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o In file included from pwiz/data/msdata/MSDataFile.cpp:26: In file included from pwiz/data/msdata/MSDataFile.hpp:30: In file included from pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o In file included from pwiz/data/identdata/IdentDataFile.cpp:25: In file included from pwiz/data/identdata/IdentDataFile.hpp:29: In file included from pwiz/data/identdata/IdentData.hpp:30: In file included from ./pwiz/data/proteome/Digestion.hpp:32: In file included from ./pwiz/data/proteome/Peptide.hpp:183: ./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o In file included from pwiz/data/identdata/IdentData.cpp:31: In file included from pwiz/data/identdata/IdentData.hpp:30: In file included from ./pwiz/data/proteome/Digestion.hpp:32: In file included from ./pwiz/data/proteome/Peptide.hpp:183: ./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o In file included from pwiz/data/identdata/DefaultReaderList.cpp:29: In file included from pwiz/data/identdata/DefaultReaderList.hpp:29: In file included from pwiz/data/identdata/Reader.hpp:28: In file included from pwiz/data/identdata/IdentData.hpp:30: In file included from ./pwiz/data/proteome/Digestion.hpp:32: In file included from ./pwiz/data/proteome/Peptide.hpp:183: ./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o In file included from pwiz/data/identdata/Reader.cpp:26: In file included from pwiz/data/identdata/Reader.hpp:28: In file included from pwiz/data/identdata/IdentData.hpp:30: In file included from ./pwiz/data/proteome/Digestion.hpp:32: In file included from ./pwiz/data/proteome/Peptide.hpp:183: ./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o In file included from pwiz/data/identdata/Serializer_protXML.cpp:28: In file included from pwiz/data/identdata/Serializer_protXML.hpp:29: In file included from pwiz/data/identdata/IdentData.hpp:30: In file included from ./pwiz/data/proteome/Digestion.hpp:32: In file included from ./pwiz/data/proteome/Peptide.hpp:183: ./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ pwiz/data/identdata/Serializer_protXML.cpp:97:9: warning: field 'strict' will be initialized after field 'nPeptides' [-Wreorder-ctor] strict(strict), ^~~~~~~~~~~~~~ SourceFilesPtr(returnValueSourceFiles) pwiz/data/identdata/Serializer_protXML.cpp:476:10: warning: private field 'readSpectrumQueries' is not used [-Wunused-private-field] bool readSpectrumQueries; ^ pwiz/data/identdata/Serializer_protXML.cpp:477:38: warning: private field 'ilr' is not used [-Wunused-private-field] const IterationListenerRegistry* ilr; ^ 4 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o In file included from pwiz/data/identdata/Serializer_pepXML.cpp:25: In file included from pwiz/data/identdata/Serializer_pepXML.hpp:27: In file included from pwiz/data/identdata/IdentData.hpp:30: In file included from ./pwiz/data/proteome/Digestion.hpp:32: In file included from ./pwiz/data/proteome/Peptide.hpp:183: ./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ pwiz/data/identdata/Serializer_pepXML.cpp:561:104: warning: adding 'char' to a string does not append to the string [-Wstring-plus-int] default: throw runtime_error("[write_search_summary] Unsupported AA residue: " + aa); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ pwiz/data/identdata/Serializer_pepXML.cpp:561:104: note: use array indexing to silence this warning default: throw runtime_error("[write_search_summary] Unsupported AA residue: " + aa); ^ & [ ] pwiz/data/identdata/Serializer_pepXML.cpp:1546:5: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ pwiz/data/identdata/Serializer_pepXML.cpp:995:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field] const CVTranslator& _cvTranslator; ^ pwiz/data/identdata/Serializer_pepXML.cpp:1450:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field] const CVTranslator& _cvTranslator; ^ pwiz/data/identdata/Serializer_pepXML.cpp:1796:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field] const CVTranslator& _cvTranslator; ^ pwiz/data/identdata/Serializer_pepXML.cpp:1970:38: warning: private field 'ilr' is not used [-Wunused-private-field] const IterationListenerRegistry* ilr; ^ 7 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o In file included from pwiz/data/identdata/Serializer_mzid.cpp:26: In file included from pwiz/data/identdata/Serializer_mzid.hpp:28: In file included from pwiz/data/identdata/IdentData.hpp:30: In file included from ./pwiz/data/proteome/Digestion.hpp:32: In file included from ./pwiz/data/proteome/Peptide.hpp:183: ./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o In file included from pwiz/data/identdata/IO.cpp:26: In file included from pwiz/data/identdata/IO.hpp:27: In file included from pwiz/data/identdata/IdentData.hpp:30: In file included from ./pwiz/data/proteome/Digestion.hpp:32: In file included from ./pwiz/data/proteome/Peptide.hpp:183: ./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o In file included from pwiz/data/identdata/References.cpp:25: In file included from pwiz/data/identdata/References.hpp:29: In file included from pwiz/data/identdata/IdentData.hpp:30: In file included from ./pwiz/data/proteome/Digestion.hpp:32: In file included from ./pwiz/data/proteome/Peptide.hpp:183: ./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ pwiz/data/identdata/References.cpp:149:13: warning: add explicit braces to avoid dangling else [-Wdangling-else] BOOST_FOREACH(OrganizationPtr& org, static_cast(c.get())->affiliations) ^ ./boost/foreach.hpp:1107:108: note: expanded from macro 'BOOST_FOREACH' if (boost::foreach_detail_::auto_any_t BOOST_FOREACH_ID(_foreach_col) = BOOST_FOREACH_CONTAIN(COL)) {} else \ ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o In file included from pwiz/data/identdata/MascotReader.cpp:26: In file included from pwiz/data/identdata/MascotReader.hpp:28: In file included from ./pwiz/data/identdata/Reader.hpp:28: In file included from pwiz/data/identdata/IdentData.hpp:30: In file included from ./pwiz/data/proteome/Digestion.hpp:32: In file included from ./pwiz/data/proteome/Peptide.hpp:183: ./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ In file included from pwiz/data/identdata/MascotReader.cpp:26: pwiz/data/identdata/MascotReader.hpp:62:11: warning: private field 'pimpl' is not used [-Wunused-private-field] Impl* pimpl; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o In file included from pwiz/data/proteome/Modification.cpp:27: pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ pwiz/data/proteome/Modification.cpp:89:5: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr formula_; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o In file included from pwiz/data/proteome/Digestion.cpp:27: In file included from pwiz/data/proteome/Digestion.hpp:32: In file included from pwiz/data/proteome/Peptide.hpp:183: pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o In file included from pwiz/data/proteome/Peptide.cpp:26: In file included from pwiz/data/proteome/Peptide.hpp:183: pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual] virtual void swap(ModificationMap&); ^ ./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map::swap' declared here: type mismatch at 1st parameter ('virtual_map::key_compare, pwiz::util::virtual_map::allocator_type> &' (aka 'virtual_map, std::allocator>> &') vs 'pwiz::proteome::ModificationMap &') virtual void swap(virtual_map& x) ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o pwiz/utility/misc/IntegerSet.cpp:307:63: warning: '&&' within '||' [-Wlogical-op-parentheses] return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ ~~ pwiz/utility/misc/IntegerSet.cpp:307:63: note: place parentheses around the '&&' expression to silence this warning return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || ^ ( ) pwiz/utility/misc/IntegerSet.cpp:308:23: warning: '&&' within '||' [-Wlogical-op-parentheses] it_==end_ && that.it_==nothing_.end()); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/utility/misc/IntegerSet.cpp:308:23: note: place parentheses around the '&&' expression to silence this warning it_==end_ && that.it_==nothing_.end()); ^ ( ) 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/BinaryData.cpp -o pwiz/utility/misc/BinaryData.o pwiz/utility/misc/BinaryData.cpp:303:9: warning: unknown pragma ignored [-Wunknown-pragmas] #pragma managed(push, off) ^ pwiz/utility/misc/BinaryData.cpp:475:9: warning: unknown pragma ignored [-Wunknown-pragmas] #pragma managed(pop) ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o pwiz/utility/misc/TabReader.cpp:44:22: warning: assigning field to itself [-Wself-assign-field] comment_char = comment_char; ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/String.cpp -o pwiz/utility/misc/String.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o mzR.so RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o -lpthread /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/mzR.buildbin-libdir/00LOCK-mzR/00new/mzR/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mzR) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR mzR.buildbin-libdir/mzR/libs/mzR.so >>>>>>> >>>>>>> Paths before fix: mzR.buildbin-libdir/mzR/libs/mzR.so: mzR.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "mzR.buildbin-libdir/mzR/libs/mzR.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "mzR.buildbin-libdir/mzR/libs/mzR.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "mzR.buildbin-libdir/mzR/libs/mzR.so" >>>>>>> Paths after fix: mzR.buildbin-libdir/mzR/libs/mzR.so: mzR.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)