mzR 1.10.8
Bernd Fischer , Steffen Neumann , Laurent Gatto , Qiang Kou
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/mzR | | Last Changed Rev: 94710 / Revision: 95116 | | Last Changed Date: 2014-09-30 07:47:22 -0700 (Tue, 30 Sep 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | [ ERROR ] | ERROR | skipped | skipped |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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###
### Running command:
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### C:\cygwin\bin\curl.exe -O http://zin2/BBS/2.14/bioc/src/contrib/mzR_1.10.8.tar.gz && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch mzR_1.10.8.tar.gz && rm mzR_1.10.8.tar.gz
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install for i386
* installing to library 'E:/biocbld/bbs-2.14-bioc/R/library'
* installing *source* package 'mzR' ...
** libs
rm -f cramp.o ramp_base64.o pwiz/data/msdata/ramp/ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./pwiz/data/msdata/Version.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/path_traits.o ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/filesystem/src/windows_file_codecvt.o ./boost/filesystem/src/codecvt_error_category.o ./boost/thread/src/win32/thread.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/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/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 ./pwiz/data/msdata/ramp/wglob.o ./random_access_gzFile.o rampR.o R_init_mzR.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c cramp.cpp -o cramp.o
cramp.h: In constructor 'cRamp::cRamp(const char*, bool)':
cramp.h:145:9: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder]
cramp.h:144:17: warning: 'rampRunInfo* cRamp::m_runInfo' [-Wreorder]
cramp.cpp:72:1: warning: when initialized here [-Wreorder]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c ramp_base64.cpp -o ramp_base64.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/ramp/ramp.cpp -o pwiz/data/msdata/ramp/ramp.o
pwiz/data/msdata/ramp/ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
pwiz/data/msdata/ramp/ramp.cpp:217:18: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
pwiz/data/msdata/ramp/ramp.cpp:394:11: warning: unused variable 'nread' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
pwiz/data/msdata/ramp/ramp.cpp:568:22: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:604:22: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:640:19: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
pwiz/data/msdata/ramp/ramp.cpp:1153:22: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
pwiz/data/msdata/ramp/ramp.cpp:1231:13: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1227:10: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
pwiz/data/msdata/ramp/ramp.cpp:1725:23: warning: unused variable 'nread' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1866:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
pwiz/data/msdata/ramp/ramp.cpp:1885:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
pwiz/data/msdata/ramp/ramp.cpp:1898:21: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1942:17: warning: unused variable 'nread' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1990:15: warning: variable 'err' set but not used [-Wunused-but-set-variable]
pwiz/data/msdata/ramp/ramp.cpp:1823:13: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
pwiz/data/msdata/ramp/ramp.cpp:2100:13: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2120:13: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2096:10: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
pwiz/data/msdata/ramp/ramp.cpp:2262:16: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2298:15: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2252:10: warning: unused variable 'fgot' [-Wunused-variable]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c RcppRamp.cpp -o RcppRamp.o
RcppRamp.cpp: In member function 'Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo()':
RcppRamp.cpp:170:21: warning: unused variable 'info' [-Wunused-variable]
RcppRamp.cpp: In member function 'Rcpp::NumericMatrix RcppRamp::get3DMap(std::vector<int>, double, double, double)':
RcppRamp.cpp:309:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c RcppRampModule.cpp -o RcppRampModule.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -D_LARGEFILE_SOURCE -I./win//i386 -D_MSC_VER -fgnu89-inline -O3 -Wall -std=gnu99 -mtune=core2 -c rnetCDF.c -o rnetCDF.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C [enabled by default]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, pwiz::minimxml::SAXParser::Handler&)':
pwiz/utility/minimxml/SAXParser.cpp:514:17: warning: 'inCDATA' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/iostreams/src/file_descriptor.cpp -o boost/iostreams/src/file_descriptor.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/filesystem/src/operations.cpp -o boost/filesystem/src/operations.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/filesystem/src/path.cpp -o boost/filesystem/src/path.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/filesystem/src/path_traits.cpp -o boost/filesystem/src/path_traits.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/filesystem/src/utf8_codecvt_facet.cpp -o boost/filesystem/src/utf8_codecvt_facet.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/filesystem/src/windows_file_codecvt.cpp -o boost/filesystem/src/windows_file_codecvt.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/filesystem/src/codecvt_error_category.cpp -o boost/filesystem/src/codecvt_error_category.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/thread/src/win32/thread.cpp -o boost/thread/src/win32/thread.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)':
pwiz/data/common/CVTranslator.cpp:134:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/common/CVTranslator.cpp:135:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/common/CVTranslator.cpp:136:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from pwiz/data/common/cv.cpp:16902:0:
pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)':
pwiz/data/common/cv.inl:102:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/thread/shared_mutex.hpp:18:0,
from ./boost/thread/detail/thread_group.hpp:9,
from ./boost/thread/thread.hpp:13,
from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/thread/win32/shared_mutex.hpp: In member function 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/thread/win32/shared_mutex.hpp:124:103: instantiated from here
./boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)':
pwiz/data/msdata/BinaryDataEncoder.cpp:284:71: warning: 'byteCount' may be used uninitialized in this function [-Wuninitialized]
pwiz/data/msdata/BinaryDataEncoder.cpp:284:71: warning: 'byteBuffer' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2013:90: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2723:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::equal(const pwiz::msdata::SpectrumIterator::Impl&) const':
pwiz/data/msdata/SpectrumIterator.cpp:126:58: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/msdata/SpectrumIterator.cpp:127:72: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::done() const':
pwiz/data/msdata/SpectrumIterator.cpp:142:48: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const':
pwiz/utility/misc/IntegerSet.cpp:308:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
pwiz/utility/misc/Filesystem.cpp:36:0: warning: "_WIN32_WINNT" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/_mingw.h:244:0: note: this is the location of the previous definition
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from ./boost/thread/shared_mutex.hpp:18:0,
from ./boost/thread/detail/thread_group.hpp:9,
from ./boost/thread/thread.hpp:13,
from ./boost/thread.hpp:13,
from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83:
./boost/thread/win32/shared_mutex.hpp: In member function 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/thread/win32/shared_mutex.hpp:124:103: instantiated from here
./boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/ramp/wglob.cpp -o pwiz/data/msdata/ramp/wglob.o
pwiz/data/msdata/ramp/wglob.cpp: In function 'int glob(const char*, int, int*, glob_t*)':
pwiz/data/msdata/ramp/wglob.cpp:63:9: warning: unused variable 'fileList' [-Wunused-variable]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c random_access_gzFile.cpp -o random_access_gzFile.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c rampR.cpp -o rampR.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -D_LARGEFILE_SOURCE -I./win//i386 -D_MSC_VER -fgnu89-inline -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_mzR.c -o R_init_mzR.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C [enabled by default]
g++ -m32 -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o pwiz/data/msdata/ramp/ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./pwiz/data/msdata/Version.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/path_traits.o ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/filesystem/src/windows_file_codecvt.o ./boost/filesystem/src/codecvt_error_category.o ./boost/thread/src/win32/thread.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/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/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 ./pwiz/data/msdata/ramp/wglob.o ./random_access_gzFile.o rampR.o R_init_mzR.o -L./win//i386 -lws2_32 -lnetcdf -lz -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lR
c:/rtools31/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lnetcdf
c:/rtools31/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lz
collect2: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'mzR'
* removing 'E:/biocbld/bbs-2.14-bioc/R/library/mzR'
* restoring previous 'E:/biocbld/bbs-2.14-bioc/R/library/mzR'
Warning: running command 'E:/biocbld/bbs-2.14-bioc/R/bin/i386/Rcmd.exe INSTALL mzR_1.10.8.tar.gz --no-multiarch' had status 1