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lesystem/src/operations.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
/bin/bash: nc-config: command not found
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c random_access_gzFile.cpp -o random_access_gzFile.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o
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g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rampR.cpp -o rampR.o
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gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_mzR.c -o R_init_mzR.o
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g++ -std=gnu++11 -shared -L/usr/local/lib/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/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/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/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/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/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 ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o -L/opt/lib/hdf5-18/lib/ -lnetcdf -L/usr/local/lib/R/lib -lR
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installing to /usr/local/lib/R/site-library/mzR/libs
** R
** inst
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** help
*** installing help indices
** building package indices
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** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (mzR)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘ropls’ ...
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** building package indices
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Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (ropls)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘pkgmaker’ ...
** package ‘pkgmaker’ successfully unpacked and MD5 sums checked
** R
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Creating meta registry in package 'pkgmaker' ... OK
Creating registry 'extra_handler' in package 'pkgmaker' ... OK
Creating registry 'extra_action' in package 'pkgmaker' ... OK
Registering extra handler 'install.packages' [function] ... OK
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
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Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘ggbeeswarm’ ...
** package ‘ggbeeswarm’ successfully unpacked and MD5 sums checked
** R
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** help
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** building package indices
** installing vignettes
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Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (ggbeeswarm)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘affy’ ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
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updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rma2.c -o rma2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rma_common.c -o rma_common.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/affy/libs
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** inst
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** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (affy)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘foreach’ ...
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** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (foreach)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘hgu133plus2.db’ ...
** R
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** help
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** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (hgu133plus2.db)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘hgu133a.db’ ...
** R
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** preparing package for lazy loading
** help
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** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (hgu133a.db)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘gdata’ ...
** package ‘gdata’ successfully unpacked and MD5 sums checked
** R
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*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (gdata)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘MassSpecWavelet’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c convolve2.c -o convolve2.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o MassSpecWavelet.so convolve2.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/MassSpecWavelet/libs
** R
** data
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** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (MassSpecWavelet)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘sandwich’ ...
** package ‘sandwich’ successfully unpacked and MD5 sums checked
** R
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** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (sandwich)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘ChemmineR’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DisjointSets.cpp -o DisjointSets.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cluster.cc -o cluster.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cstrsplit.cc -o cstrsplit.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c desc.cc -o desc.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fingerprints.cc -o fingerprints.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c formats.cc -o formats.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c molecule.cc -o molecule.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c r_wrap.cc -o r_wrap.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c script.cc -o script.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c similarity.cc -o similarity.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/ChemmineR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (ChemmineR)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘e1071’ ...
** package ‘e1071’ successfully unpacked and MD5 sums checked
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
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** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rsvm.c -o Rsvm.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cmeans.c -o cmeans.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cshell.c -o cshell.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c floyd.c -o floyd.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c svm.cpp -o svm.o
svm.cpp: In function ‘svm_model* svm_load_model(const char*)’:
svm.cpp:2788:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fp,"%80s",cmd);
                        ^
svm.cpp:2792:25: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%80s",cmd);
                         ^
svm.cpp:2817:25: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%80s",cmd);
                         ^
svm.cpp:2841:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%d",&param.degree);
                                 ^
svm.cpp:2843:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%lf",&param.gamma);
                                 ^
svm.cpp:2845:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%lf",&param.coef0);
                                 ^
svm.cpp:2847:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%d",&model->nr_class);
                                    ^
svm.cpp:2849:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%d",&model->l);
                             ^
svm.cpp:2855:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%lf",&model->rho[i]);
                                    ^
svm.cpp:2862:37: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%d",&model->label[i]);
                                     ^
svm.cpp:2869:38: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%lf",&model->probA[i]);
                                      ^
svm.cpp:2876:38: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%lf",&model->probB[i]);
                                      ^
svm.cpp:2883:35: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%d",&model->nSV[i]);
                                   ^
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o e1071.so Rsvm.o cmeans.o cshell.o floyd.o init.o svm.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/e1071/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (e1071)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘topGO’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (topGO)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘edgeR’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_add_prior_count.cpp -o R_add_prior_count.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_add_repeat_matrices.cpp -o R_add_repeat_matrices.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_calculate_cpm.cpp -o R_calculate_cpm.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_check_counts.cpp -o R_check_counts.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_compute_apl.cpp -o R_compute_apl.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_compute_nbdev.cpp -o R_compute_nbdev.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_levenberg.cpp -o R_levenberg.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_loess_by_col.cpp -o R_loess_by_col.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_one_group.cpp -o R_one_group.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c add_prior.cpp -o add_prior.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c adj_coxreid.cpp -o adj_coxreid.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fmm_spline.c -o fmm_spline.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glm_levenberg.cpp -o glm_levenberg.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glm_one_group.cpp -o glm_one_group.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.cpp -o init.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c interpolator.cpp -o interpolator.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matvec_check.cpp -o matvec_check.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nbdev.cpp -o nbdev.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o edgeR.so R_add_prior_count.o R_add_repeat_matrices.o R_ave_log_cpm.o R_calculate_cpm.o R_check_counts.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_get_one_way_fitted.o R_initialize_levenberg.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -L/usr/local/lib/R/lib -lRlapack -lopenblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/edgeR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (edgeR)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘HTMLUtils’ ...
** package ‘HTMLUtils’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (HTMLUtils)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘safe’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (safe)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘KEGGREST’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (KEGGREST)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘pracma’ ...
** package ‘pracma’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** demo
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (pracma)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘Rmpfr’ ...
** package ‘Rmpfr’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking mpfr.h usability... yes
checking mpfr.h presence... yes
checking for mpfr.h... yes
checking gmp.h usability... yes
checking gmp.h presence... yes
checking for gmp.h... yes
checking for __gmpz_init in -lgmp... yes
checking for mpfr_init in -lmpfr... yes
checking for mpfr_digamma in -lmpfr... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Ops.c -o Ops.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Summary.c -o Summary.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c convert.c -o convert.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Rmpfr.so Ops.o Summary.o convert.o init.o utils.o -lmpfr -lgmp -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/Rmpfr/libs
** R
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘factorial’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘diag’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘diag<-’ from package ‘base’ in package ‘Rmpfr’
Creating a new generic function for ‘cbind’ in package ‘Rmpfr’
Creating a new generic function for ‘rbind’ in package ‘Rmpfr’
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘colMeans’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘rowMeans’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘norm’ from package ‘base’ in package ‘Rmpfr’
in method for ‘show’ with signature ‘"integrateR"’: no definition for class “integrateR”
Creating a new generic function for ‘pmin’ in package ‘Rmpfr’
Creating a new generic function for ‘pmax’ in package ‘Rmpfr’
Creating a generic function for ‘atan2’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘beta’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘lbeta’ from package ‘base’ in package ‘Rmpfr’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (Rmpfr)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘ALS’ ...
** package ‘ALS’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (ALS)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘ChemometricsWithR’ ...
** package ‘ChemometricsWithR’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (ChemometricsWithR)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘doParallel’ ...
** package ‘doParallel’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (doParallel)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘rngtools’ ...
** package ‘rngtools’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (rngtools)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘vsn’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vsn.c -o vsn.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vsn2.c -o vsn2.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o vsn.so init.o vsn.o vsn2.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/vsn/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (vsn)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘scater’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c calc_exprs.cpp -o calc_exprs.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.cpp -o init.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matrix_info.cpp -o matrix_info.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.cpp -o utils.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o scater.so calc_exprs.o init.o matrix_info.o utils.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/scater/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a new generic function for ‘mutate’ in package ‘scater’
Creating a new generic function for ‘filter’ in package ‘scater’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (scater)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘gage’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (gage)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘gplots’ ...
** package ‘gplots’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (gplots)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘maxLik’ ...
** package ‘maxLik’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (maxLik)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘bioassayR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘organism’ in package ‘bioassayR’
Creating a new generic function for ‘organism<-’ in package ‘bioassayR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (bioassayR)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘biosigner’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (biosigner)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘pathview’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (pathview)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘RankProd’ ...
** R
** data
** inst
** preparing package for lazy loading
[1] "this is the new version of the RankProd package"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (RankProd)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘tofsims’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c LapackEigen.cpp -o LapackEigen.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c c_importer.cpp -o c_importer.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nn.cpp -o nn.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c readRawPhi.cpp -o readRawPhi.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tofsims_init.c -o tofsims_init.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utilities.cpp -o utilities.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o tofsims.so LapackEigen.o RcppExports.o c_importer.o nn.o readRawPhi.o tofsims_init.o utilities.o -llapack -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/tofsims/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (tofsims)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘mzID’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (mzID)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘doRNG’ ...
** package ‘doRNG’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (doRNG)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘Glimma’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (Glimma)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘MSnbase’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Spectrum1_class.c -o Spectrum1_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Spectrum2_class.c -o Spectrum2_class.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** inst
** preparing package for lazy loading
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (MSnbase)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘PADOG’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (PADOG)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘xcms’ ...
** libs
rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/SegProc.cpp -o massifquant/SegProc.o
In file included from massifquant/SegProc.h:4:0,
                 from massifquant/SegProc.cpp:10:
massifquant/SegProc.cpp: In member function ‘double SegProc::Rf_pt(double, double, int, int)’:
massifquant/nmath.h:77:26: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
 #define _(String) (String)
                          ^
massifquant/nmath.h:125:21: note: in expansion of macro ‘_’
         char *msg = _(""); \
                     ^
massifquant/nmath.h:117:29: note: in expansion of macro ‘ML_ERROR’
 #define ML_ERR_return_NAN { ML_ERROR(ME_DOMAIN, ""); return ML_NAN; }
                             ^
massifquant/SegProc.cpp:361:19: note: in expansion of macro ‘ML_ERR_return_NAN’
     if (n <= 0.0) ML_ERR_return_NAN;
                   ^
massifquant/nmath.h:128:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
                             msg = _("argument out of domain in '%s'\n"); \
                                 ^
massifquant/nmath.h:117:29: note: in expansion of macro ‘ML_ERROR’
 #define ML_ERR_return_NAN { ML_ERROR(ME_DOMAIN, ""); return ML_NAN; }
                             ^
massifquant/SegProc.cpp:361:19: note: in expansion of macro ‘ML_ERR_return_NAN’
     if (n <= 0.0) ML_ERR_return_NAN;
                   ^
massifquant/nmath.h:131:32: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
                            msg = _("value out of range in '%s'\n"); \
                                ^
massifquant/nmath.h:117:29: note: in expansion of macro ‘ML_ERROR’
 #define ML_ERR_return_NAN { ML_ERROR(ME_DOMAIN, ""); return ML_NAN; }
                             ^
massifquant/SegProc.cpp:361:19: note: in expansion of macro ‘ML_ERR_return_NAN’
     if (n <= 0.0) ML_ERR_return_NAN;
                   ^
massifquant/nmath.h:134:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
                             msg = _("convergence failed in '%s'\n"); \
                                 ^
massifquant/nmath.h:117:29: note: in expansion of macro ‘ML_ERROR’
 #define ML_ERR_return_NAN { ML_ERROR(ME_DOMAIN, ""); return ML_NAN; }
                             ^
massifquant/SegProc.cpp:361:19: note: in expansion of macro ‘ML_ERR_return_NAN’
     if (n <= 0.0) ML_ERR_return_NAN;
                   ^
massifquant/nmath.h:137:36: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
                                msg = _("full precision may not have been achieved in '%s'\n"); \
                                    ^
massifquant/nmath.h:117:29: note: in expansion of macro ‘ML_ERROR’
 #define ML_ERR_return_NAN { ML_ERROR(ME_DOMAIN, ""); return ML_NAN; }
                             ^
massifquant/SegProc.cpp:361:19: note: in expansion of macro ‘ML_ERR_return_NAN’
     if (n <= 0.0) ML_ERR_return_NAN;
                   ^
massifquant/nmath.h:140:36: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
                                msg = _("underflow occurred in '%s'\n"); \
                                    ^
massifquant/nmath.h:117:29: note: in expansion of macro ‘ML_ERROR’
 #define ML_ERR_return_NAN { ML_ERROR(ME_DOMAIN, ""); return ML_NAN; }
                             ^
massifquant/SegProc.cpp:361:19: note: in expansion of macro ‘ML_ERR_return_NAN’
     if (n <= 0.0) ML_ERR_return_NAN;
                   ^
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c obiwarp/mat.cpp -o obiwarp/mat.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c obiwarp/vec.cpp -o obiwarp/vec.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastMatch.c -o fastMatch.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mzClust_hclust.c -o mzClust_hclust.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mzROI.c -o mzROI.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c util.c -o util.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xcms.c -o xcms.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c binners.c -o binners.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/xcms/libs
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘sigma’ in package ‘xcms’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (xcms)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘EGSEA’ ...
** R
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EGSEA)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘proFIA’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c UtilFunc.c -o UtilFunc.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastMatchPpm.c -o fastMatchPpm.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o proFIA.so FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/proFIA/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (proFIA)

The downloaded source packages are in
	‘/tmp/RtmpEYkwnr/downloaded_packages’
Old packages: 'AnnotationHub', 'Biostrings', 'DelayedArray', 'ensembldb',
  'GenomicAlignments', 'IRanges', 'R6', 'S4Vectors'
> 
> # just in case there were warnings, we want to see them
> # without having to scroll up:
> warnings()
NULL
> 
> if (!is.null(warnings()))
+ {
+     w <- capture.output(warnings())
+     if (length(grep("is not available|had non-zero exit status", w)))
+         quit("no", 1L)
+ }
> 
> suppressWarnings(BiocInstaller::biocValid(fix=TRUE, ask=FALSE))

* sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.12.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.27.2

loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0   

* Out-of-date packages
                  Package             LibPath                         Installed
AnnotationHub     "AnnotationHub"     "/usr/local/lib/R/site-library" "2.9.1"  
Biostrings        "Biostrings"        "/usr/local/lib/R/site-library" "2.45.0" 
DelayedArray      "DelayedArray"      "/usr/local/lib/R/site-library" "0.3.4"  
ensembldb         "ensembldb"         "/usr/local/lib/R/site-library" "2.1.3"  
GenomicAlignments "GenomicAlignments" "/usr/local/lib/R/site-library" "1.13.1" 
IRanges           "IRanges"           "/usr/local/lib/R/site-library" "2.11.1" 
R6                "R6"                "/usr/local/lib/R/site-library" "2.2.0"  
S4Vectors         "S4Vectors"         "/usr/local/lib/R/site-library" "0.15.1" 
                  Built   ReposVer
AnnotationHub     "3.4.0" "2.9.3" 
Biostrings        "3.4.0" "2.45.1"
DelayedArray      "3.4.0" "0.3.5" 
ensembldb         "3.4.0" "2.1.4" 
GenomicAlignments "3.4.0" "1.13.2"
IRanges           "3.4.0" "2.11.2"
R6                "3.4.0" "2.2.1" 
S4Vectors         "3.4.0" "0.15.2"
                  Repository                                              
AnnotationHub     "https://bioconductor.org/packages/3.6/bioc/src/contrib"
Biostrings        "https://bioconductor.org/packages/3.6/bioc/src/contrib"
DelayedArray      "https://bioconductor.org/packages/3.6/bioc/src/contrib"
ensembldb         "https://bioconductor.org/packages/3.6/bioc/src/contrib"
GenomicAlignments "https://bioconductor.org/packages/3.6/bioc/src/contrib"
IRanges           "https://bioconductor.org/packages/3.6/bioc/src/contrib"
R6                "https://cran.rstudio.com/src/contrib"                  
S4Vectors         "https://bioconductor.org/packages/3.6/bioc/src/contrib"

update with biocLite()

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.27.2), R 3.4.0 (2017-04-21).
Installing package(s) ‘AnnotationHub’, ‘Biostrings’, ‘DelayedArray’,
  ‘ensembldb’, ‘GenomicAlignments’, ‘IRanges’, ‘R6’, ‘S4Vectors’
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/AnnotationHub_2.9.3.tar.gz'
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Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘R6’ ...
** package ‘R6’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (R6)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘S4Vectors’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c AEbufs.c -o AEbufs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DataFrame_class.c -o DataFrame_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Hits_class.c -o Hits_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c LLint_class.c -o LLint_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c List_class.c -o List_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rle_class.c -o Rle_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rle_utils.c -o Rle_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SEXP_utils.c -o SEXP_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SimpleList_class.c -o SimpleList_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c eval_utils.c -o eval_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c hash_utils.c -o hash_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c int_utils.c -o int_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c logical_utils.c -o logical_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c safe_arithm.c -o safe_arithm.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sort_utils.c -o sort_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c str_utils.c -o str_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c subsetting_utils.c -o subsetting_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vector_utils.c -o vector_utils.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o eval_utils.o hash_utils.o int_utils.o logical_utils.o safe_arithm.o sort_utils.o str_utils.o subsetting_utils.o vector_utils.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/S4Vectors/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
Creating a generic function for ‘%in%’ from package ‘base’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"data.table","DataFrame"’: no definition for class “data.table”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (S4Vectors)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘AnnotationHub’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (AnnotationHub)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘IRanges’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c NCList.c -o NCList.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Ranges_class.c -o Ranges_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Ranges_comparison.c -o Ranges_comparison.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c coverage_methods.c -o coverage_methods.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c inter_range_methods.c -o inter_range_methods.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘ifelse’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (IRanges)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c MIndex_class.c -o MIndex_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XStringSetList_class.c -o XStringSetList_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XStringSet_io.c -o XStringSet_io.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XString_class.c -o XString_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c align_needwunsQS.c -o align_needwunsQS.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c align_utils.c -o align_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c letter_frequency.c -o letter_frequency.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lowlevel_matching.c -o lowlevel_matching.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern_indels.c -o match_pattern_indels.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict.c -o match_pdict.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict_utils.c -o match_pdict_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c replaceAt.c -o replaceAt.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c replace_letter_at.c -o replace_letter_at.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c strutils.c -o strutils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c translate.c -o translate.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xscat.c -o xscat.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/Biostrings/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘strsplit’ in package ‘Biostrings’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’
Creating a new generic function for ‘offset’ in package ‘Biostrings’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (Biostrings)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘DelayedArray’ ...
** R
** inst
** preparing package for lazy loading
in method for ‘coerce’ with signature ‘"DelayedMatrix","dgCMatrix"’: no definition for class “dgCMatrix”
in method for ‘coerce’ with signature ‘"DelayedMatrix","sparseMatrix"’: no definition for class “sparseMatrix”
Creating a new generic function for ‘apply’ in package ‘DelayedArray’
Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a new generic function for ‘rowMaxs’ in package ‘DelayedArray’
Creating a new generic function for ‘colMaxs’ in package ‘DelayedArray’
Creating a new generic function for ‘rowMins’ in package ‘DelayedArray’
Creating a new generic function for ‘colMins’ in package ‘DelayedArray’
Creating a new generic function for ‘rowRanges’ in package ‘DelayedArray’
Creating a new generic function for ‘colRanges’ in package ‘DelayedArray’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (DelayedArray)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘ensembldb’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (ensembldb)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘GenomicAlignments’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cigar_utils.c -o cigar_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/GenomicAlignments/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (GenomicAlignments)

The downloaded source packages are in
	‘/tmp/RtmpEYkwnr/downloaded_packages’
> 
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Removing intermediate container 5b49784acfd2
Successfully built 4bf94d9a28bd
[container-bioc_devel_protmetcore] $ docker tag 4bf94d9a28bd docker-registry-v2.local:30750/bioconductor/devel_protmetcore2:latest
[container-bioc_devel_protmetcore] $ docker inspect 4bf94d9a28bd
[container-bioc_devel_protmetcore] $ docker push docker-registry-v2.local:30750/bioconductor/devel_protmetcore2:devel
The push refers to a repository [docker-registry-v2.local:30750/bioconductor/devel_protmetcore2]
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[container-bioc_devel_protmetcore] $ docker push docker-registry-v2.local:30750/bioconductor/devel_protmetcore2:latest
The push refers to a repository [docker-registry-v2.local:30750/bioconductor/devel_protmetcore2]
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latest: digest: sha256:c83e50dbc81a28ebdb1dfa28ddf3e75f58093dd0269461c6fdd2e1580ddfc782 size: 4285
Warning: you have no plugins providing access control for builds, so falling back to legacy behavior of permitting any downstream builds to be triggered
Triggering a new build of container-bioc_devel_metabolomics
Finished: SUCCESS