############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL affxparser ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'affxparser' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' rm -f fusion/calvin_files/data/src/CDFData.o fusion/calvin_files/data/src/CDFProbeGroupInformation.o fusion/calvin_files/data/src/CDFProbeInformation.o fusion/calvin_files/data/src/CDFProbeSetInformation.o fusion/calvin_files/data/src/CDFQCProbeInformation.o fusion/calvin_files/data/src/CDFQCProbeSetInformation.o fusion/calvin_files/data/src/CELData.o fusion/calvin_files/data/src/CHPBackgroundZone.o fusion/calvin_files/data/src/CHPData.o fusion/calvin_files/data/src/CHPExpressionEntry.o fusion/calvin_files/data/src/CHPMultiDataData.o fusion/calvin_files/data/src/CHPTilingData.o fusion/calvin_files/data/src/CHPQuantificationData.o fusion/calvin_files/data/src/CHPQuantificationDetectionData.o fusion/calvin_files/data/src/CHPGenotypeEntry.o fusion/calvin_files/data/src/CHPUniversalEntry.o fusion/calvin_files/data/src/ColumnInfo.o fusion/calvin_files/data/src/DataGroup.o fusion/calvin_files/data/src/DataGroupHeader.o fusion/calvin_files/data/src/DataSet.o fusion/calvin_files/data/src/DataSetHeader.o fusion/calvin_files/data/src/FileHeader.o fusion/calvin_files/data/src/GenericData.o fusion/calvin_files/data/src/GenericDataHeader.o fusion/calvin_files/exception/src/ExceptionBase.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionBPMAPData.o fusion/calvin_files/fusion/src/FusionCDFData.o fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion/calvin_files/fusion/src/FusionCELData.o fusion/calvin_files/fusion/src/FusionCHPData.o fusion/calvin_files/fusion/src/FusionProbeSetResults.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionCHPLegacyData.o fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion/calvin_files/fusion/src/FusionCHPTilingData.o fusion/calvin_files/fusion/src/FusionCHPGenericData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion/calvin_files/parameter/src/ParameterNameValueType.o fusion/calvin_files/parsers/src/CDFFileReader.o fusion/calvin_files/parsers/src/CelFileReader.o fusion/calvin_files/parsers/src/CHPFileReader.o fusion/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion/calvin_files/parsers/src/CHPTilingFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion/calvin_files/parsers/src/DataGroupHeaderReader.o fusion/calvin_files/parsers/src/DataGroupReader.o fusion/calvin_files/parsers/src/DataSetHeaderReader.o fusion/calvin_files/parsers/src/DataSetReader.o fusion/calvin_files/parsers/src/FileHeaderReader.o fusion/calvin_files/parsers/src/FileInput.o fusion/calvin_files/parsers/src/GenericDataHeaderReader.o fusion/calvin_files/parsers/src/GenericFileReader.o fusion/calvin_files/utils/src/AffymetrixGuid.o fusion/calvin_files/utils/src/DateTime.o fusion/calvin_files/utils/src/FileUtils.o fusion/calvin_files/utils/src/StringUtils.o fusion/calvin_files/utils/src/checksum.o fusion/file/BPMAPFileData.o fusion/file/BPMAPFileWriter.o fusion/file/CDFFileData.o fusion/file/CELFileData.o fusion/file/CHPFileData.o fusion/file/FileIO.o fusion/file/FileWriter.o fusion/file/TsvFile/ClfFile.o fusion/file/TsvFile/PgfFile.o fusion/file/TsvFile/TsvFile.o fusion/util/AffxByteArray.o fusion/util/AffxConv.o fusion/util/MsgStream.o fusion/util/Util.o fusion/util/Err.o fusion/util/Fs.o fusion/util/Verbose.o fusion/util/RowFile.o fusion/util/TableFile.o fusion/util/Convert.o R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o R_affx_clf_pgf_parser.o R_affx_chp_parser.o 000.init.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CDFData.cpp -o fusion/calvin_files/data/src/CDFData.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/DataGroup.h:31, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion/calvin_files/data/src/CDFData.h:26, from fusion/calvin_files/data/src/CDFData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\stdlib.h:36, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\mm_malloc.h:27, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\xmmintrin.h:34, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\immintrin.h:31, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\x86intrin.h:32, from c:\rtools43\x86_64-w64-mingw32.static.posix\include\winnt.h:1555, from c:\rtools43\x86_64-w64-mingw32.static.posix\include\minwindef.h:163, from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windef.h:9, from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:69: c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\cstdlib:137:11: error: 'at_quick_exit' has not been declared in '::' 137 | using ::at_quick_exit; | ^~~~~~~~~~~~~ c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\cstdlib:160:11: error: 'quick_exit' has not been declared in '::' 160 | using ::quick_exit; | ^~~~~~~~~~ c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\stdlib.h:43:14: error: 'at_quick_exit' has not been declared in 'std' 43 | using std::at_quick_exit; | ^~~~~~~~~~~~~ c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\stdlib.h:46:14: error: 'quick_exit' has not been declared in 'std' 46 | using std::quick_exit; | ^~~~~~~~~~ make: *** [Makevars.win:7: fusion/calvin_files/data/src/CDFData.o] Error 1 ERROR: compilation failed for package 'affxparser' * removing 'F:/biocbuild/bbs-3.17-bioc/R/library/affxparser'