BioC 3.3: INSTALL report for mzR on zin2

Package: mzR

Version: 2.6.3

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD INSTALL mzR

StartedAt: 2016-10-12 18:10:22 -0700 (Wed, 12 Oct 2016)

EndedAt: 2016-10-12 18:20:33 -0700 (Wed, 12 Oct 2016)

EllapsedTime: 610.7 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD INSTALL mzR
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* installing to library ‘/home/biocbuild/bbs-3.3-bioc/R/library’
* installing *source* package ‘mzR’ ...
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/pthread/once.o ./boost/thread/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.o ./pwiz/data/msdata/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/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.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_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.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/RAMPAdapter.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/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/Version.o ./pwiz/data/identdata/References.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/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 ./random_access_gzFile.o ./RcppExports.o rampR.o R_init_mzR.o
find . -name \*˜ -exec rm {} \;   ## from cleanup
find . -name \*.o -exec rm {} \;  ## from cleanup
find . -name "#*#" -exec rm {} \; ## from cleanup
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c cramp.cpp -o cramp.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c ramp_base64.cpp -o ramp_base64.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c ramp.cpp -o ramp.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppRamp.cpp -o RcppRamp.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppRampModule.cpp -o RcppRampModule.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c rnetCDF.c -o rnetCDF.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppPwiz.cpp -o RcppPwiz.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppPwizModule.cpp -o RcppPwizModule.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppIdent.cpp -o RcppIdent.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppIdentModule.cpp -o RcppIdentModule.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/iostreams/src/file_descriptor.cpp -o boost/iostreams/src/file_descriptor.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/thread/pthread/once.cpp -o boost/thread/pthread/once.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/thread/pthread/thread.cpp -o boost/thread/pthread/thread.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/filesystem/src/operations.cpp -o boost/filesystem/src/operations.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/filesystem/src/path.cpp -o boost/filesystem/src/path.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/filesystem/src/utf8_codecvt_facet.cpp -o boost/filesystem/src/utf8_codecvt_facet.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c random_access_gzFile.cpp -o random_access_gzFile.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c rampR.cpp -o rampR.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c R_init_mzR.c -o R_init_mzR.o
g++ -std=c++11 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o mzR.so cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/pthread/once.o ./boost/thread/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.o ./pwiz/data/msdata/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/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.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_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.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/RAMPAdapter.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/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/Version.o ./pwiz/data/identdata/References.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/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 ./random_access_gzFile.o ./RcppExports.o rampR.o R_init_mzR.o -lpthread -L/usr/local/lib -lnetcdf -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/R/library/mzR/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘close’ from package ‘base’ in package ‘mzR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mzR)