##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf mzR.buildbin-libdir && mkdir mzR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mzR_2.30.0.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_2.30.0.tar.gz'
>>>>>>> 

* installing *source* package ‘mzR’ ...
** using staged installation
** libs
rm -f RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<pwiz::data::MemoryIndex::Impl>' 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<pwiz::data::MemoryIndex::Impl>' 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<pwiz::data::MemoryIndex::Impl, pwiz::data::MemoryIndex::Impl>' 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<pwiz::data::MemoryIndex::Impl>::shared_ptr<pwiz::data::MemoryIndex::Impl>' requested here
PWIZ_API_DECL MemoryIndex::MemoryIndex() : impl_(new Impl) {}
                                           ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
pwiz/data/common/CVTranslator.cpp:133:53: warning: '&&' within '||' [-Wlogical-op-parentheses]
    return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ ~~
pwiz/data/common/CVTranslator.cpp:133:53: 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:134:40: 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:134:40: 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:135:40: warning: '&&' within '||' [-Wlogical-op-parentheses]
            key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:135:40: 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:136:40: warning: '&&' within '||' [-Wlogical-op-parentheses]
            key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:136:40: 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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<pwiz::data::BinaryIndexStream::Impl>' 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<pwiz::data::BinaryIndexStream::Impl>' 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<pwiz::data::BinaryIndexStream::Impl, pwiz::data::BinaryIndexStream::Impl>' 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<pwiz::data::BinaryIndexStream::Impl>::shared_ptr<pwiz::data::BinaryIndexStream::Impl>' requested here
PWIZ_API_DECL BinaryIndexStream::BinaryIndexStream(shared_ptr<iostream> isPtr) : impl_(new Impl(isPtr)) {}
                                                                                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
In file included from pwiz/data/msdata/Serializer_MGF.cpp:29:
In file included from ./boost/spirit/include/karma.hpp:16:
In file included from ./boost/spirit/home/karma.hpp:13:
In file included from ./boost/spirit/home/karma/char.hpp:13:
In file included from ./boost/spirit/home/karma/char/char.hpp:14:
In file included from ./boost/spirit/home/support/common_terminals.hpp:15:
In file included from ./boost/spirit/home/support/terminal.hpp:17:
In file included from ./boost/spirit/home/support/meta_compiler.hpp:17:
In file included from ./boost/spirit/home/support/make_component.hpp:17:
In file included from ./boost/phoenix/core/actor.hpp:24:
In file included from ./boost/proto/extends.hpp:31:
./boost/proto/expr.hpp:140:44: warning: unknown warning group '-Wdeprecated-copy', ignored [-Wunknown-warning-option]
            #pragma GCC diagnostic ignored "-Wdeprecated-copy"
                                           ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/SpectrumListBase.cpp -o pwiz/data/msdata/SpectrumListBase.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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 <boost/bind/bind.hpp> + 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)))
                                 ^
<scratch space>:250:2: note: expanded from here
 message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " "<boost/bind/bind.hpp> + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.")
 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
pwiz/data/msdata/MSData.cpp:1115:1: warning: control may reach end of non-void function [-Wreturn-type]
}
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
In file included from pwiz/data/identdata/IdentData.cpp:32:
In file included from ./boost/xpressive/xpressive_dynamic.hpp:17:
In file included from ./boost/xpressive/regex_compiler.hpp:30:
In file included from ./boost/xpressive/basic_regex.hpp:28:
In file included from ./boost/xpressive/detail/static/grammar.hpp:19:
In file included from ./boost/proto/core.hpp:17:
./boost/proto/expr.hpp:140:44: warning: unknown warning group '-Wdeprecated-copy', ignored [-Wunknown-warning-option]
            #pragma GCC diagnostic ignored "-Wdeprecated-copy"
                                           ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
In file included from pwiz/data/identdata/Serializer_protXML.cpp:41:
In file included from ./boost/xpressive/xpressive.hpp:18:
In file included from ./boost/xpressive/xpressive_static.hpp:24:
In file included from ./boost/xpressive/regex_primitives.hpp:28:
In file included from ./boost/proto/core.hpp:17:
./boost/proto/expr.hpp:140:44: warning: unknown warning group '-Wdeprecated-copy', ignored [-Wunknown-warning-option]
            #pragma GCC diagnostic ignored "-Wdeprecated-copy"
                                           ^
pwiz/data/identdata/Serializer_protXML.cpp:97:9: warning: field 'strict' will be initialized after field 'nPeptides' [-Wreorder]
        strict(strict),
        ^
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;
                                     ^
5 warnings generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
In file included from pwiz/data/identdata/Serializer_pepXML.cpp:37:
In file included from ./boost/xpressive/xpressive_dynamic.hpp:17:
In file included from ./boost/xpressive/regex_compiler.hpp:30:
In file included from ./boost/xpressive/basic_regex.hpp:28:
In file included from ./boost/xpressive/detail/static/grammar.hpp:19:
In file included from ./boost/proto/core.hpp:17:
./boost/proto/expr.hpp:140:44: warning: unknown warning group '-Wdeprecated-copy', ignored [-Wunknown-warning-option]
            #pragma GCC diagnostic ignored "-Wdeprecated-copy"
                                           ^
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: control may reach end of non-void function [-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;
                                     ^
8 warnings generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
pwiz/data/identdata/References.cpp:149:13: warning: add explicit braces to avoid dangling else [-Wdangling-else]
            BOOST_FOREACH(OrganizationPtr& org, static_cast<Person*>(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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
pwiz/data/proteome/Modification.cpp:89:5: warning: 'auto_ptr<pwiz::chemistry::Formula>' is deprecated [-Wdeprecated-declarations]
    auto_ptr<Formula> formula_;
    ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<pwiz::chemistry::Formula>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
In file included from pwiz/data/proteome/Digestion.cpp:34:
In file included from ./boost/xpressive/xpressive_dynamic.hpp:17:
In file included from ./boost/xpressive/regex_compiler.hpp:30:
In file included from ./boost/xpressive/basic_regex.hpp:28:
In file included from ./boost/xpressive/detail/static/grammar.hpp:19:
In file included from ./boost/proto/core.hpp:17:
./boost/proto/expr.hpp:140:44: warning: unknown warning group '-Wdeprecated-copy', ignored [-Wunknown-warning-option]
            #pragma GCC diagnostic ignored "-Wdeprecated-copy"
                                           ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > > &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
In file included from pwiz/utility/minimxml/XMLWriter.cpp:29:
In file included from ./boost/spirit/include/karma.hpp:16:
In file included from ./boost/spirit/home/karma.hpp:13:
In file included from ./boost/spirit/home/karma/char.hpp:13:
In file included from ./boost/spirit/home/karma/char/char.hpp:14:
In file included from ./boost/spirit/home/support/common_terminals.hpp:15:
In file included from ./boost/spirit/home/support/terminal.hpp:17:
In file included from ./boost/spirit/home/support/meta_compiler.hpp:17:
In file included from ./boost/spirit/home/support/make_component.hpp:17:
In file included from ./boost/phoenix/core/actor.hpp:24:
In file included from ./boost/proto/extends.hpp:31:
./boost/proto/expr.hpp:140:44: warning: unknown warning group '-Wdeprecated-copy', ignored [-Wunknown-warning-option]
            #pragma GCC diagnostic ignored "-Wdeprecated-copy"
                                           ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
In file included from pwiz/utility/minimxml/SAXParser.cpp:31:
In file included from ./boost/xpressive/xpressive_dynamic.hpp:17:
In file included from ./boost/xpressive/regex_compiler.hpp:30:
In file included from ./boost/xpressive/basic_regex.hpp:28:
In file included from ./boost/xpressive/detail/static/grammar.hpp:19:
In file included from ./boost/proto/core.hpp:17:
./boost/proto/expr.hpp:140:44: warning: unknown warning group '-Wdeprecated-copy', ignored [-Wunknown-warning-option]
            #pragma GCC diagnostic ignored "-Wdeprecated-copy"
                                           ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/misc/BinaryData.cpp -o pwiz/utility/misc/BinaryData.o
pwiz/utility/misc/BinaryData.cpp:302:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma managed(push, off)
        ^
pwiz/utility/misc/BinaryData.cpp:474:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma managed(pop)
        ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
In file included from pwiz/utility/misc/Filesystem.cpp:58:
In file included from ./boost/spirit/include/karma.hpp:16:
In file included from ./boost/spirit/home/karma.hpp:13:
In file included from ./boost/spirit/home/karma/char.hpp:13:
In file included from ./boost/spirit/home/karma/char/char.hpp:14:
In file included from ./boost/spirit/home/support/common_terminals.hpp:15:
In file included from ./boost/spirit/home/support/terminal.hpp:17:
In file included from ./boost/spirit/home/support/meta_compiler.hpp:17:
In file included from ./boost/spirit/home/support/make_component.hpp:17:
In file included from ./boost/phoenix/core/actor.hpp:24:
In file included from ./boost/proto/extends.hpp:31:
./boost/proto/expr.hpp:140:44: warning: unknown warning group '-Wdeprecated-copy', ignored [-Wunknown-warning-option]
            #pragma GCC diagnostic ignored "-Wdeprecated-copy"
                                           ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwiz/utility/misc/String.cpp -o pwiz/utility/misc/String.o
In file included from pwiz/utility/misc/String.cpp:24:
In file included from ./boost/spirit/include/karma.hpp:16:
In file included from ./boost/spirit/home/karma.hpp:13:
In file included from ./boost/spirit/home/karma/char.hpp:13:
In file included from ./boost/spirit/home/karma/char/char.hpp:14:
In file included from ./boost/spirit/home/support/common_terminals.hpp:15:
In file included from ./boost/spirit/home/support/terminal.hpp:17:
In file included from ./boost/spirit/home/support/meta_compiler.hpp:17:
In file included from ./boost/spirit/home/support/make_component.hpp:17:
In file included from ./boost/phoenix/core/actor.hpp:24:
In file included from ./boost/proto/extends.hpp:31:
./boost/proto/expr.hpp:140:44: warning: unknown warning group '-Wdeprecated-copy', ignored [-Wunknown-warning-option]
            #pragma GCC diagnostic ignored "-Wdeprecated-copy"
                                           ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mzR.so RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o -lpthread /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.15-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 LINKS FOR mzR.buildbin-libdir/mzR/libs/mzR.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "mzR.buildbin-libdir/mzR/libs/mzR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/lib/libquadmath.0.dylib" "mzR.buildbin-libdir/mzR/libs/mzR.so"