############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL mzR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘mzR’ ... ** this is package ‘mzR’ version ‘2.41.1’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 rm -f RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppPwiz.cpp -o RcppPwiz.o RcppPwiz.cpp: In member function ‘Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector)’: RcppPwiz.cpp:408:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 408 | Rprintf("Index whichScan out of bounds [1 ... %d].\n", n_scans); | ~^ ~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld RcppPwiz.cpp: In member function ‘Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)’: RcppPwiz.cpp:854:55: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 854 | Rprintf("Index whichChrom out of bounds [0 ... %d].\n", (clp->size())-1); | ~^ ~~~~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppPwizModule.cpp -o RcppPwizModule.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppIdent.cpp -o RcppIdent.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppIdentModule.cpp -o RcppIdentModule.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o In file included from ./boost/functional/hash.hpp:6, from ./boost/thread/detail/thread.hpp:41, from ./boost/thread/thread_only.hpp:22, from ./boost/thread/thread.hpp:12, from pwiz/data/common/BinaryIndexStream.cpp:27: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from pwiz/data/common/Index.hpp:27, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/mz5/../SpectrumListBase.hpp:30, from pwiz/data/msdata/mz5/../SpectrumList_mz5.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:27: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from pwiz/data/msdata/mz5/../../common/cv.hpp:35, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:27, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:30: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/stdexcept:39, from ./pwiz/utility/misc/Exception.hpp:28, from ./pwiz/utility/misc/Std.hpp:28, from pwiz/data/msdata/DefaultReaderList.cpp:26: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:28: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:29, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_mz5.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:29: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/stdexcept:39, from ./pwiz/utility/misc/Exception.hpp:28, from ./pwiz/utility/misc/Std.hpp:28, from pwiz/data/msdata/Serializer_mz5.cpp:26: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/Serializer_MGF.cpp:26: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:26: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/SpectrumListBase.cpp -o pwiz/data/msdata/SpectrumListBase.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumListBase.cpp:25: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ./boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from ./boost/smart_ptr/detail/yield_k.hpp:23, from ./boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from ./boost/smart_ptr/detail/spinlock.hpp:42, from ./boost/smart_ptr/detail/spinlock_pool.hpp:25, from ./boost/smart_ptr/shared_ptr.hpp:29, from ./boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:30: ./boost/config/pragma_message.hpp:24:34: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ ./boost/bind.hpp:36:1: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_mz5.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:28: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/stdexcept:39, from ./pwiz/utility/misc/Exception.hpp:28, from ./pwiz/utility/misc/Std.hpp:28, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:31: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o In file included from ./boost/functional/hash.hpp:6, from ./boost/multi_index/detail/hash_index_args.hpp:17, from ./boost/multi_index/hashed_index_fwd.hpp:16, from ./boost/multi_index/hashed_index.hpp:43, from ./pwiz/utility/misc/mru_list.hpp:26, from pwiz/data/msdata/MemoryMRUCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.hpp:28, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o In file included from ./boost/functional/hash.hpp:6, from ./pwiz/data/msdata/SpectrumListBase.hpp:30, from ./pwiz/data/msdata/SpectrumListWrapper.hpp:28, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:27: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/stdexcept:39, from ./pwiz/utility/misc/Exception.hpp:28, from ./pwiz/utility/misc/Std.hpp:28, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o pwiz/data/proteome/Modification.cpp:89:5: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 89 | auto_ptr formula_; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ./boost/smart_ptr/detail/sp_counted_impl.hpp:35, from ./boost/smart_ptr/detail/shared_count.hpp:27, from ./boost/smart_ptr/shared_ptr.hpp:17, from ./boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/BinaryData.cpp -o pwiz/utility/misc/BinaryData.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o In file included from ./boost/functional/hash.hpp:6, from ./boost/thread/detail/thread.hpp:41, from ./boost/thread/thread_only.hpp:22, from ./boost/thread/thread.hpp:12, from ./boost/thread.hpp:13, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:77: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/locale:41, from ./boost/iostreams/detail/config/codecvt.hpp:63, from ./boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/String.cpp -o pwiz/utility/misc/String.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o In file included from ./boost/functional/hash.hpp:6, from ./boost/thread/detail/thread.hpp:41, from ./boost/thread/thread_only.hpp:22, from boost/libs/thread/src/pthread/thread.cpp:11: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from ./boost/thread/exceptions.hpp:20, from ./boost/thread/pthread/thread_data.hpp:10, from ./boost/thread/thread_only.hpp:17: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o mzR.so RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o -lpthread /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-mzR/00new/mzR/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mzR)