############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/affxparser_1.64.1.tar.gz && rm -rf affxparser.buildbin-libdir && mkdir affxparser.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affxparser.buildbin-libdir affxparser_1.64.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL affxparser_1.64.1.zip && rm affxparser_1.64.1.tar.gz affxparser_1.64.1.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 1 877k 1 16227 0 0 136k 0 0:00:06 --:--:-- 0:00:06 136k 100 877k 100 877k 0 0 2552k 0 --:--:-- --:--:-- --:--:-- 2551k install for i386 * installing *source* package 'affxparser' ... ** using staged installation ** libs rm -f fusion_sdk/calvin_files/data/src/CDFData.o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o fusion_sdk/calvin_files/data/src/CELData.o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o fusion_sdk/calvin_files/data/src/CHPData.o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o fusion_sdk/calvin_files/data/src/CHPMultiDataData.o fusion_sdk/calvin_files/data/src/CHPTilingData.o fusion_sdk/calvin_files/data/src/CHPQuantificationData.o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o fusion_sdk/calvin_files/data/src/ColumnInfo.o fusion_sdk/calvin_files/data/src/DataGroup.o fusion_sdk/calvin_files/data/src/DataGroupHeader.o fusion_sdk/calvin_files/data/src/DataSet.o fusion_sdk/calvin_files/data/src/DataSetHeader.o fusion_sdk/calvin_files/data/src/FileHeader.o fusion_sdk/calvin_files/data/src/GenericData.o fusion_sdk/calvin_files/data/src/GenericDataHeader.o fusion_sdk/calvin_files/exception/src/ExceptionBase.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion_sdk/calvin_files/fusion/src/FusionCELData.o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o fusion_sdk/calvin_files/parsers/src/CelFileReader.o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataSetReader.o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o fusion_sdk/calvin_files/parsers/src/FileInput.o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o fusion_sdk/calvin_files/utils/src/DateTime.o fusion_sdk/calvin_files/utils/src/FileUtils.o fusion_sdk/calvin_files/utils/src/StringUtils.o fusion_sdk/calvin_files/utils/src/checksum.o fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o fusion_sdk/file/CHPFileData.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o fusion_sdk/file/TsvFile/ClfFile.o fusion_sdk/file/TsvFile/PgfFile.o fusion_sdk/file/TsvFile/TsvFile.o fusion_sdk/util/AffxByteArray.o fusion_sdk/util/AffxConv.o fusion_sdk/util/MsgStream.o fusion_sdk/util/Util.o fusion_sdk/util/Err.o fusion_sdk/util/Fs.o fusion_sdk/util/Verbose.o fusion_sdk/util/RowFile.o fusion_sdk/util/TableFile.o fusion_sdk/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 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CDFData.cpp -o fusion_sdk/calvin_files/data/src/CDFData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/data/src/CDFData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/data/src/CDFData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataSet.h:28, from fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:30, from fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:27, from fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataSet.h:28, from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.h:27, from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/DataSet.h:25, from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.h:27, from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataSet.h:28, from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.h:31, from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.h:25, from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CELData.cpp -o fusion_sdk/calvin_files/data/src/CELData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/data/src/CELData.h:26, from fusion_sdk/calvin_files/data/src/CELData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/data/src/CELData.h:26, from fusion_sdk/calvin_files/data/src/CELData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPBackgroundZone.cpp -o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPData.cpp -o fusion_sdk/calvin_files/data/src/CHPData.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPExpressionEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp -o fusion_sdk/calvin_files/data/src/CHPMultiDataData.o fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp: In member function 'void affymetrix_calvin_io::CHPMultiDataData::SetEntryCount(affymetrix_calvin_io::MultiDataType, int32_t, int32_t, const std::vector&, const wstring&)': fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:427:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:429:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' DataGroupHeader* dgHdr = GetDataGroupHeader(dataTypeGroupNames[dataType]); ^~~~~~~~~~~~~~~ fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp: In member function 'void affymetrix_calvin_io::CHPMultiDataData::SetEntryCount(affymetrix_calvin_io::MultiDataType, int32_t, int, int, int, const wstring&)': fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:457:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:459:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' DataGroupHeader* dgHdr = GetDataGroupHeader(dataTypeGroupNames[dataType]); ^~~~~~~~~~~~~~~ fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp: In member function 'void affymetrix_calvin_io::CHPMultiDataData::SetEntryCount(affymetrix_calvin_io::MultiDataType, int32_t, int, int, int, int, const wstring&)': fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:482:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:484:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' DataGroupHeader* dgHdr = GetDataGroupHeader(dataTypeGroupNames[dataType]); ^~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPTilingData.cpp -o fusion_sdk/calvin_files/data/src/CHPTilingData.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp -o fusion_sdk/calvin_files/data/src/CHPQuantificationData.o fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp: In member function 'void affymetrix_calvin_io::CHPQuantificationData::AddColumns(affymetrix_calvin_io::DataSetHeader&, bool)': fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp:144:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp:146:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' hdr.AddFloatColumn(QUANTIFICATION_QUANTIFICATION_NAME); ^~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp -o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp: In member function 'void affymetrix_calvin_io::CHPQuantificationDetectionData::AddColumns(affymetrix_calvin_io::DataSetHeader&, bool)': fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp:151:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp:153:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' hdr.AddFloatColumn(QUANTIFICATION_DETECTION_QUANTIFICATION_NAME); ^~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPUniversalEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/ColumnInfo.cpp -o fusion_sdk/calvin_files/data/src/ColumnInfo.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/DataGroup.cpp -o fusion_sdk/calvin_files/data/src/DataGroup.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/DataGroup.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/DataGroup.h:28, from fusion_sdk/calvin_files/data/src/DataGroup.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp -o fusion_sdk/calvin_files/data/src/DataGroupHeader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/DataSet.cpp -o fusion_sdk/calvin_files/data/src/DataSet.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataSet.h:28, from fusion_sdk/calvin_files/data/src/DataSet.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/DataSet.h:25, from fusion_sdk/calvin_files/data/src/DataSet.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/DataSetHeader.cpp -o fusion_sdk/calvin_files/data/src/DataSetHeader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/FileHeader.cpp -o fusion_sdk/calvin_files/data/src/FileHeader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/GenericData.cpp -o fusion_sdk/calvin_files/data/src/GenericData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/data/src/GenericData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/data/src/GenericData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp -o fusion_sdk/calvin_files/data/src/GenericDataHeader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/exception/src/ExceptionBase.cpp -o fusion_sdk/calvin_files/exception/src/ExceptionBase.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/data/src/CELData.h:26, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.h:27, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp:22: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/data/src/CELData.h:26, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.h:27, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp:22: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/CDFFileData.h:37, from fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/file/CDFFileData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27, from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27, from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp -o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:27, from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:27, from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.h:25, from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.h:25, from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp -o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/parameter/src/ParameterException.h:24, from fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.h:27, from fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:24: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/parsers/src/CDFFileReader.h:29, from fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/parsers/src/CDFFileReader.h:29, from fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CelFileReader.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/data/src/CELData.h:26, from fusion_sdk/calvin_files/parsers/src/CelFileReader.h:27, from fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/data/src/CELData.h:26, from fusion_sdk/calvin_files/parsers/src/CelFileReader.h:27, from fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CHPFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.h:27, from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.h:27, from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.h:27, from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.h:27, from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/DataSetReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataSetReader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/FileInput.cpp -o fusion_sdk/calvin_files/parsers/src/FileInput.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/parsers/src/FileInput.h:27, from fusion_sdk/calvin_files/parsers/src/FileInput.cpp:24: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/parsers/src/FileInput.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:27, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:27, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp -o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/utils/src/checksum.h:27, from fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp:26: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/utils/src/DateTime.cpp -o fusion_sdk/calvin_files/utils/src/DateTime.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/utils/src/FileUtils.cpp -o fusion_sdk/calvin_files/utils/src/FileUtils.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Fs.h:27, from fusion_sdk/calvin_files/utils/src/FileUtils.cpp:26: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/utils/src/FileUtils.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/utils/src/StringUtils.cpp -o fusion_sdk/calvin_files/utils/src/StringUtils.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/utils/src/checksum.cpp -o fusion_sdk/calvin_files/utils/src/checksum.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/BPMAPFileData.cpp -o fusion_sdk/file/BPMAPFileData.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/FileIO.h:27, from fusion_sdk/file/BPMAPFileData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/file/BPMAPFileData.h:30, from fusion_sdk/file/BPMAPFileData.cpp:20: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/BPMAPFileWriter.cpp -o fusion_sdk/file/BPMAPFileWriter.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/FileIO.h:27, from fusion_sdk/file/BPMAPFileWriter.cpp:22: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/file/BPMAPFileData.h:30, from fusion_sdk/file/BPMAPFileWriter.h:26, from fusion_sdk/file/BPMAPFileWriter.cpp:20: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/CDFFileData.cpp -o fusion_sdk/file/CDFFileData.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/CDFFileData.h:37, from fusion_sdk/file/CDFFileData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/file/CDFFileData.h:31, from fusion_sdk/file/CDFFileData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 fusion_sdk/file/CDFFileData.cpp: In member function 'bool affxcdf::CCDFFileData::ReadTextFormat()': fusion_sdk/file/CDFFileData.cpp:858:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] else if ( strncmp( subStr, CDFVERSION6, strlen(CDFVERSION6)) == 0) ^~ fusion_sdk/file/CDFFileData.cpp:861:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (m_Header.m_Version >= 6) ^~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/CELFileData.cpp -o fusion_sdk/file/CELFileData.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/CHPFileData.cpp -o fusion_sdk/file/CHPFileData.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/CHPFileData.h:36, from fusion_sdk/file/CHPFileData.cpp:20: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw32/i686-w64-mingw32/include/string.h:9, from C:/rtools40/mingw32/include/c++/8.3.0/cstring:42, from fusion_sdk/file/TagValuePair.h:27, from fusion_sdk/file/CHPFileData.h:34, from fusion_sdk/file/CHPFileData.cpp:20: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/FileIO.cpp -o fusion_sdk/file/FileIO.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/FileIO.h:27, from fusion_sdk/file/FileIO.cpp:26: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/file/FileIO.cpp:23: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/FileIO.h:27, from fusion_sdk/file/FileWriter.h:26, from fusion_sdk/file/FileWriter.cpp:25: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/file/FileWriter.cpp:22: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/TsvFile/ClfFile.cpp -o fusion_sdk/file/TsvFile/ClfFile.o In file included from fusion_sdk/file/TsvFile/ClfFile.h:31, from fusion_sdk/file/TsvFile/ClfFile.cpp:27: fusion_sdk/file/TsvFile/TsvFile.h: In member function 'affx::TsvFile& affx::TsvFile::operator=(const affx::TsvFile&)': fusion_sdk/file/TsvFile/TsvFile.h:527:6: warning: statement has no effect [-Wunused-value] (that); /* unused var */ ~^~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/TsvFile/PgfFile.cpp -o fusion_sdk/file/TsvFile/PgfFile.o In file included from fusion_sdk/file/TsvFile/PgfFile.h:32, from fusion_sdk/file/TsvFile/PgfFile.cpp:274: fusion_sdk/file/TsvFile/TsvFile.h: In member function 'affx::TsvFile& affx::TsvFile::operator=(const affx::TsvFile&)': fusion_sdk/file/TsvFile/TsvFile.h:527:6: warning: statement has no effect [-Wunused-value] (that); /* unused var */ ~^~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/TsvFile/TsvFile.cpp -o fusion_sdk/file/TsvFile/TsvFile.o In file included from fusion_sdk/file/TsvFile/TsvFile.cpp:24: fusion_sdk/file/TsvFile/TsvFile.h: In member function 'affx::TsvFile& affx::TsvFile::operator=(const affx::TsvFile&)': fusion_sdk/file/TsvFile/TsvFile.h:527:6: warning: statement has no effect [-Wunused-value] (that); /* unused var */ ~^~~~~ fusion_sdk/file/TsvFile/TsvFile.cpp: In static member function 'static int affx::TsvFile::getLineCountInFile(const string&, bool)': fusion_sdk/file/TsvFile/TsvFile.cpp:4921:20: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] catch (exception e) { ^ fusion_sdk/file/TsvFile/TsvFile.cpp: In static member function 'static int affx::TsvFile::replaceCharInFile(const string&, char, char, bool)': fusion_sdk/file/TsvFile/TsvFile.cpp:4970:20: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] catch (exception e) { ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/AffxByteArray.cpp -o fusion_sdk/util/AffxByteArray.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Convert.h:32, from fusion_sdk/util/Err.h:34, from fusion_sdk/util/AffxString.h:29, from fusion_sdk/util/AffxByteArray.h:29, from fusion_sdk/util/AffxByteArray.cpp:27: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw32/i686-w64-mingw32/include/string.h:9, from C:/rtools40/mingw32/include/c++/8.3.0/cstring:42, from fusion_sdk/util/AffxConv.h:33, from fusion_sdk/util/AffxByteArray.h:28, from fusion_sdk/util/AffxByteArray.cpp:27: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 fusion_sdk/util/AffxByteArray.cpp: In member function 'const AffxByteArray& AffxByteArray::operator=(const AffxByteArray&)': fusion_sdk/util/AffxByteArray.cpp:320:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (this == &ba) ^~ fusion_sdk/util/AffxByteArray.cpp:323:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' empty(); ^~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/AffxConv.cpp -o fusion_sdk/util/AffxConv.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Convert.h:32, from fusion_sdk/util/AffxConv.cpp:34: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw32/i686-w64-mingw32/include/string.h:9, from C:/rtools40/mingw32/include/c++/8.3.0/cstring:42, from fusion_sdk/util/AffxConv.h:33, from fusion_sdk/util/AffxConv.cpp:32: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 fusion_sdk/util/AffxConv.cpp: In function 'std::__cxx11::string getInt(int, bool)': fusion_sdk/util/AffxConv.cpp:124:8: warning: self-comparison always evaluates to false [-Wtautological-compare] if (i != i) {return "nan";} ~~^~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/MsgStream.cpp -o fusion_sdk/util/MsgStream.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Convert.h:32, from fusion_sdk/util/Err.h:34, from fusion_sdk/util/MsgStream.cpp:33: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw32/i686-w64-mingw32/include/string.h:9, from C:/rtools40/mingw32/include/c++/8.3.0/cstring:42, from fusion_sdk/util/MsgHandler.h:31, from fusion_sdk/util/MsgStream.h:32, from fusion_sdk/util/MsgStream.cpp:31: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/Util.cpp -o fusion_sdk/util/Util.o fusion_sdk/util/Util.cpp:220: warning: "S_IRWXG" redefined #define S_IRWXG 00070 //mask for group permissions In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:158: note: this is the location of the previous definition #define S_IRWXG (S_IRWXU >> 3) fusion_sdk/util/Util.cpp:221: warning: "S_IRGRP" redefined #define S_IRGRP 00040 //group has read permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:155: note: this is the location of the previous definition #define S_IRGRP (S_IRUSR >> 3) fusion_sdk/util/Util.cpp:222: warning: "S_IWGRP" redefined #define S_IWGRP 00020 //group has write permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:156: note: this is the location of the previous definition #define S_IWGRP (S_IWUSR >> 3) fusion_sdk/util/Util.cpp:223: warning: "S_IXGRP" redefined #define S_IXGRP 00010 //group has execute permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:157: note: this is the location of the previous definition #define S_IXGRP (S_IXUSR >> 3) fusion_sdk/util/Util.cpp:224: warning: "S_IRWXO" redefined #define S_IRWXO 00007 //mask for permissions for others (not in group) In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:163: note: this is the location of the previous definition #define S_IRWXO (S_IRWXG >> 3) fusion_sdk/util/Util.cpp:225: warning: "S_IROTH" redefined #define S_IROTH 00004 //others have read permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:160: note: this is the location of the previous definition #define S_IROTH (S_IRGRP >> 3) fusion_sdk/util/Util.cpp:226: warning: "S_IWOTH" redefined #define S_IWOTH 00002 //others have write permisson In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:161: note: this is the location of the previous definition #define S_IWOTH (S_IWGRP >> 3) fusion_sdk/util/Util.cpp:227: warning: "S_IXOTH" redefined #define S_IXOTH 00001 // others have execute permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:162: note: this is the location of the previous definition #define S_IXOTH (S_IXGRP >> 3) "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/Err.cpp -o fusion_sdk/util/Err.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/Fs.cpp -o fusion_sdk/util/Fs.o fusion_sdk/util/Fs.cpp:43: warning: "S_IRUSR" redefined #define S_IRUSR 00400 //owner has read permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:152: note: this is the location of the previous definition #define S_IRUSR _S_IRUSR fusion_sdk/util/Fs.cpp:44: warning: "S_IWUSR" redefined #define S_IWUSR 00200 //owner has write permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:151: note: this is the location of the previous definition #define S_IWUSR _S_IWUSR fusion_sdk/util/Fs.cpp:45: warning: "S_IXUSR" redefined #define S_IXUSR 00100 ///owner has execute permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:150: note: this is the location of the previous definition #define S_IXUSR _S_IXUSR fusion_sdk/util/Fs.cpp:46: warning: "S_IRWXG" redefined #define S_IRWXG 00070 //mask for group permissions In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:158: note: this is the location of the previous definition #define S_IRWXG (S_IRWXU >> 3) fusion_sdk/util/Fs.cpp:47: warning: "S_IRGRP" redefined #define S_IRGRP 00040 //group has read permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:155: note: this is the location of the previous definition #define S_IRGRP (S_IRUSR >> 3) fusion_sdk/util/Fs.cpp:48: warning: "S_IWGRP" redefined #define S_IWGRP 00020 //group has write permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:156: note: this is the location of the previous definition #define S_IWGRP (S_IWUSR >> 3) fusion_sdk/util/Fs.cpp:49: warning: "S_IXGRP" redefined #define S_IXGRP 00010 //group has execute permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:157: note: this is the location of the previous definition #define S_IXGRP (S_IXUSR >> 3) fusion_sdk/util/Fs.cpp:50: warning: "S_IRWXO" redefined #define S_IRWXO 00007 //mask for permissions for others (not in group) In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:163: note: this is the location of the previous definition #define S_IRWXO (S_IRWXG >> 3) fusion_sdk/util/Fs.cpp:51: warning: "S_IROTH" redefined #define S_IROTH 00004 //others have read permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:160: note: this is the location of the previous definition #define S_IROTH (S_IRGRP >> 3) fusion_sdk/util/Fs.cpp:52: warning: "S_IWOTH" redefined #define S_IWOTH 00002 //others have write permisson In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:161: note: this is the location of the previous definition #define S_IWOTH (S_IWGRP >> 3) fusion_sdk/util/Fs.cpp:53: warning: "S_IXOTH" redefined #define S_IXOTH 00001 // others have execute permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw32/i686-w64-mingw32/include/sys/stat.h:162: note: this is the location of the previous definition #define S_IXOTH (S_IXGRP >> 3) fusion_sdk/util/Fs.cpp: In static member function 'static AptErr_t Fs::listDir(const string&, std::vector >&, bool)': fusion_sdk/util/Fs.cpp:1028:9: warning: unused variable 'rv' [-Wunused-variable] DWORD rv=0; ^~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/Verbose.cpp -o fusion_sdk/util/Verbose.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Fs.h:27, from fusion_sdk/util/Verbose.cpp:31: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw32/i686-w64-mingw32/include/string.h:9, from C:/rtools40/mingw32/include/c++/8.3.0/cstring:42, from fusion_sdk/calvin_files/utils/src/StringUtils.h:27, from fusion_sdk/util/Verbose.cpp:29: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/RowFile.cpp -o fusion_sdk/util/RowFile.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Convert.h:32, from fusion_sdk/util/RowFile.cpp:30: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw32/i686-w64-mingw32/include/string.h:9, from C:/rtools40/mingw32/include/c++/8.3.0/cstring:42, from fusion_sdk/util/RowFile.h:31, from fusion_sdk/util/RowFile.cpp:28: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/TableFile.cpp -o fusion_sdk/util/TableFile.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Util.h:35, from fusion_sdk/util/TableFile.h:32, from fusion_sdk/util/TableFile.cpp:28: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw32/i686-w64-mingw32/include/string.h:9, from C:/rtools40/mingw32/include/c++/8.3.0/cstring:42, from fusion_sdk/util/RowFile.h:31, from fusion_sdk/util/TableFile.h:31, from fusion_sdk/util/TableFile.cpp:28: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/Convert.cpp -o fusion_sdk/util/Convert.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c R_affx_cel_parser.cpp -o R_affx_cel_parser.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27, from R_affx_cel_parser.cpp:1: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27, from R_affx_cel_parser.cpp:1: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R.h:91, from R_affx_cel_parser.cpp:9: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:55: warning: "ERROR" redefined #define ERROR ),error(R_problem_buf);} In file included from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:71, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27, from R_affx_cel_parser.cpp:1: C:/rtools40/mingw32/i686-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition #define ERROR 0 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c R_affx_cdf_parser.cpp -o R_affx_cdf_parser.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_parser.cpp:1: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_parser.cpp:1: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R.h:91, from R_affx_cdf_parser.cpp:9: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:55: warning: "ERROR" redefined #define ERROR ),error(R_problem_buf);} In file included from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:71, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_parser.cpp:1: C:/rtools40/mingw32/i686-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition #define ERROR 0 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c R_affx_cdf_extras.cpp -o R_affx_cdf_extras.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_extras.cpp:1: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_extras.cpp:1: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R.h:91, from R_affx_cdf_extras.cpp:8: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:55: warning: "ERROR" redefined #define ERROR ),error(R_problem_buf);} In file included from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:71, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_extras.cpp:1: C:/rtools40/mingw32/i686-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition #define ERROR 0 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c R_affx_bpmap_parser.cpp -o R_affx_bpmap_parser.o In file included from R_affx_bpmap_parser.cpp:4: R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/file/BPMAPFileData.h:30, from R_affx_bpmap_parser.cpp:1: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R.h:91, from R_affx_bpmap_parser.cpp:11: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:55: warning: "ERROR" redefined #define ERROR ),error(R_problem_buf);} In file included from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:71, from fusion_sdk/file/BPMAPFileData.h:30, from R_affx_bpmap_parser.cpp:1: C:/rtools40/mingw32/i686-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition #define ERROR 0 R_affx_bpmap_parser.cpp: In function 'SEXPREC* R_affx_get_bpmap_file(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': R_affx_bpmap_parser.cpp:482:32: warning: 'centerpos' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(centerpos)[j] = seqHit.getCenterPosition(); ~~~~~~~^~~~~~~~~~~ R_affx_bpmap_parser.cpp:479:36: warning: 'startpos' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(startpos)[j] = seqHit.getStartPosition(); ~~~~~~~^~~~~~~~~~ R_affx_bpmap_parser.cpp:485:33: warning: 'matchscore' may be used uninitialized in this function [-Wmaybe-uninitialized] REAL(matchscore)[j] = (double)seqHit.MatchScore; ~~~~^~~~~~~~~~~~ R_affx_bpmap_parser.cpp:488:32: warning: 'probelength' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(probelength)[j] = (int)seqHit.ProbeLength; ~~~~~~~^~~~~~~~~~~~~ R_affx_bpmap_parser.cpp:467:32: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(strand)[j] = (unsigned int)seqHit.TopStrand; ~~~~~~~^~~~~~~~ R_affx_bpmap_parser.cpp:475:41: warning: 'probeseq' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_STRING_ELT(probeseq, j, mkChar(cstr)); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ R_affx_bpmap_parser.cpp:502:39: warning: 'mmy' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(seqObj, kk, mmy); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ R_affx_bpmap_parser.cpp:463:32: warning: 'mmx' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(mmx)[j] = seqHit.MMX; ~~~~~~~^~~~~ R_affx_bpmap_parser.cpp:495:35: warning: 'pmy' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(seqObj, kk, pmy); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ R_affx_bpmap_parser.cpp:493:35: warning: 'pmx' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(seqObj, kk, pmx); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c R_affx_clf_pgf_parser.cpp -o R_affx_clf_pgf_parser.o In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:39, from R_affx_clf_pgf_parser.cpp:11: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:55: warning: "ERROR" redefined #define ERROR ),error(R_problem_buf);} In file included from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:71, from fusion_sdk/portability/affy-base-types.h:56, from fusion_sdk/file/TsvFile/TsvFile.h:30, from fusion_sdk/file/TsvFile/ClfFile.h:31, from R_affx_clf_pgf_parser.cpp:2: C:/rtools40/mingw32/i686-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition #define ERROR 0 In file included from fusion_sdk/file/TsvFile/ClfFile.h:31, from R_affx_clf_pgf_parser.cpp:2: fusion_sdk/file/TsvFile/TsvFile.h: In member function 'affx::TsvFile& affx::TsvFile::operator=(const affx::TsvFile&)': fusion_sdk/file/TsvFile/TsvFile.h:527:6: warning: statement has no effect [-Wunused-value] (that); /* unused var */ ~^~~~~ R_affx_clf_pgf_parser.cpp: In function 'SEXPREC* R_affx_get_clf_file(SEXP, SEXP, SEXP)': R_affx_clf_pgf_parser.cpp:284:21: warning: catching polymorphic type 'class Except' by value [-Wcatch-value=] } catch (Except ex) { ^~ R_affx_clf_pgf_parser.cpp: In function 'SEXPREC* R_affx_get_pgf_file(SEXP, SEXP, SEXP, SEXP)': R_affx_clf_pgf_parser.cpp:327:21: warning: catching polymorphic type 'class Except' by value [-Wcatch-value=] } catch (Except ex) { ^~ R_affx_clf_pgf_parser.cpp: In function 'void R_affx_get_body(affx::PgfFile*, SEXP, SEXP)': R_affx_clf_pgf_parser.cpp:161:23: warning: 'pindices' may be used uninitialized in this function [-Wmaybe-uninitialized] currIndex = pindices[i]; ~~~~~~~~~~^~~~~~~~~~~~~ R_affx_clf_pgf_parser.cpp:132:4: warning: 'currIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] if (nProbesets < currIndex) continue; ^~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c R_affx_chp_parser.cpp -o R_affx_chp_parser.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from R_affx_chp_parser.cpp:1: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from R_affx_chp_parser.cpp:1: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:39, from R_affx_chp_parser.cpp:21: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:55: warning: "ERROR" redefined #define ERROR ),error(R_problem_buf);} In file included from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:71, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from R_affx_chp_parser.cpp:1: C:/rtools40/mingw32/i686-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition #define ERROR 0 In file included from R_affx_chp_parser.cpp:21: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h: In function 'SEXPREC* R_affx_GetCHPGenotypingResults(affymetrix_fusion_io::FusionCHPLegacyData*)': C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:142:46: warning: 'nocall' may be used uninitialized in this function [-Wmaybe-uninitialized] #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) ^ R_affx_chp_parser.cpp:318:38: note: 'nocall' was declared here SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; ^~~~~~ In file included from R_affx_chp_parser.cpp:21: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:142:46: warning: 'bb' may be used uninitialized in this function [-Wmaybe-uninitialized] #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) ^ R_affx_chp_parser.cpp:318:34: note: 'bb' was declared here SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; ^~ In file included from R_affx_chp_parser.cpp:21: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:142:46: warning: 'ab' may be used uninitialized in this function [-Wmaybe-uninitialized] #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) ^ R_affx_chp_parser.cpp:318:30: note: 'ab' was declared here SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; ^~ In file included from R_affx_chp_parser.cpp:21: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:142:46: warning: 'aa' may be used uninitialized in this function [-Wmaybe-uninitialized] #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) ^ R_affx_chp_parser.cpp:318:26: note: 'aa' was declared here SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; ^~ In file included from R_affx_chp_parser.cpp:21: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:142:46: warning: 'ras1' may be used uninitialized in this function [-Wmaybe-uninitialized] #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) ^ R_affx_chp_parser.cpp:318:14: note: 'ras1' was declared here SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; ^~~~ R_affx_chp_parser.cpp:360:11: warning: 'ras2' may be used uninitialized in this function [-Wmaybe-uninitialized] REAL(ras2)[i] = f.GetRAS2(); ~~~~^~~~~~ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o affxparser.dll tmp.def fusion_sdk/calvin_files/data/src/CDFData.o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o fusion_sdk/calvin_files/data/src/CELData.o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o fusion_sdk/calvin_files/data/src/CHPData.o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o fusion_sdk/calvin_files/data/src/CHPMultiDataData.o fusion_sdk/calvin_files/data/src/CHPTilingData.o fusion_sdk/calvin_files/data/src/CHPQuantificationData.o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o fusion_sdk/calvin_files/data/src/ColumnInfo.o fusion_sdk/calvin_files/data/src/DataGroup.o fusion_sdk/calvin_files/data/src/DataGroupHeader.o fusion_sdk/calvin_files/data/src/DataSet.o fusion_sdk/calvin_files/data/src/DataSetHeader.o fusion_sdk/calvin_files/data/src/FileHeader.o fusion_sdk/calvin_files/data/src/GenericData.o fusion_sdk/calvin_files/data/src/GenericDataHeader.o fusion_sdk/calvin_files/exception/src/ExceptionBase.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion_sdk/calvin_files/fusion/src/FusionCELData.o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o fusion_sdk/calvin_files/parsers/src/CelFileReader.o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataSetReader.o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o fusion_sdk/calvin_files/parsers/src/FileInput.o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o fusion_sdk/calvin_files/utils/src/DateTime.o fusion_sdk/calvin_files/utils/src/FileUtils.o fusion_sdk/calvin_files/utils/src/StringUtils.o fusion_sdk/calvin_files/utils/src/checksum.o fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o fusion_sdk/file/CHPFileData.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o fusion_sdk/file/TsvFile/ClfFile.o fusion_sdk/file/TsvFile/PgfFile.o fusion_sdk/file/TsvFile/TsvFile.o fusion_sdk/util/AffxByteArray.o fusion_sdk/util/AffxConv.o fusion_sdk/util/MsgStream.o fusion_sdk/util/Util.o fusion_sdk/util/Err.o fusion_sdk/util/Fs.o fusion_sdk/util/Verbose.o fusion_sdk/util/RowFile.o fusion_sdk/util/TableFile.o fusion_sdk/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 -lws2_32 -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/affxparser.buildbin-libdir/00LOCK-affxparser/00new/affxparser/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'affxparser' finding HTML links ... done 1._Dictionary html 2._Cell_coordinates_and_cell_indices html 9._Advanced_-_Cell-index_maps_for_reading_and_writing html affxparser-package html applyCdfGroupFields html applyCdfGroups html arrangeCelFilesByChipType html cdfAddBaseMmCounts html cdfAddPlasqTypes html cdfAddProbeOffsets html cdfGetFields html cdfGetGroups html cdfGtypeCelToPQ html cdfHeaderToCelHeader html cdfMergeAlleles html cdfMergeStrands html cdfMergeToQuartets html cdfOrderBy html cdfOrderColumnsBy html cdfSetDimension html compareCdfs html compareCels html convertCdf html convertCel html copyCel html createCel html findCdf html findFiles html invertMap html isCelFile html parseDatHeaderString html readBpmap html readCcg html readCcgHeader html readCdf html readCdfCellIndices html readCdfDataFrame html readCdfGroupNames html readCdfHeader html readCdfIsPm html readCdfNbrOfCellsPerUnitGroup html readCdfQc html readCdfUnitNames html readCdfUnits html readCdfUnitsWriteMap html readCel html readCelHeader html readCelIntensities html readCelRectangle html readCelUnits html readChp html readClf html readClfEnv html readClfHeader html readPgf html readPgfEnv html readPgfHeader html updateCel html updateCelUnits html writeCdf html writeCdfHeader html writeCdfQcUnits html writeCdfUnits html writeCelHeader html writeTpmap html ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'affxparser' ... ** libs rm -f fusion_sdk/calvin_files/data/src/CDFData.o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o fusion_sdk/calvin_files/data/src/CELData.o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o fusion_sdk/calvin_files/data/src/CHPData.o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o fusion_sdk/calvin_files/data/src/CHPMultiDataData.o fusion_sdk/calvin_files/data/src/CHPTilingData.o fusion_sdk/calvin_files/data/src/CHPQuantificationData.o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o fusion_sdk/calvin_files/data/src/ColumnInfo.o fusion_sdk/calvin_files/data/src/DataGroup.o fusion_sdk/calvin_files/data/src/DataGroupHeader.o fusion_sdk/calvin_files/data/src/DataSet.o fusion_sdk/calvin_files/data/src/DataSetHeader.o fusion_sdk/calvin_files/data/src/FileHeader.o fusion_sdk/calvin_files/data/src/GenericData.o fusion_sdk/calvin_files/data/src/GenericDataHeader.o fusion_sdk/calvin_files/exception/src/ExceptionBase.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion_sdk/calvin_files/fusion/src/FusionCELData.o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o fusion_sdk/calvin_files/parsers/src/CelFileReader.o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataSetReader.o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o fusion_sdk/calvin_files/parsers/src/FileInput.o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o fusion_sdk/calvin_files/utils/src/DateTime.o fusion_sdk/calvin_files/utils/src/FileUtils.o fusion_sdk/calvin_files/utils/src/StringUtils.o fusion_sdk/calvin_files/utils/src/checksum.o fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o fusion_sdk/file/CHPFileData.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o fusion_sdk/file/TsvFile/ClfFile.o fusion_sdk/file/TsvFile/PgfFile.o fusion_sdk/file/TsvFile/TsvFile.o fusion_sdk/util/AffxByteArray.o fusion_sdk/util/AffxConv.o fusion_sdk/util/MsgStream.o fusion_sdk/util/Util.o fusion_sdk/util/Err.o fusion_sdk/util/Fs.o fusion_sdk/util/Verbose.o fusion_sdk/util/RowFile.o fusion_sdk/util/TableFile.o fusion_sdk/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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CDFData.cpp -o fusion_sdk/calvin_files/data/src/CDFData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/data/src/CDFData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/data/src/CDFData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataSet.h:28, from fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:30, from fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:27, from fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataSet.h:28, from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.h:27, from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/DataSet.h:25, from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.h:27, from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataSet.h:28, from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.h:31, from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.h:25, from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CELData.cpp -o fusion_sdk/calvin_files/data/src/CELData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/data/src/CELData.h:26, from fusion_sdk/calvin_files/data/src/CELData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/data/src/CELData.h:26, from fusion_sdk/calvin_files/data/src/CELData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPBackgroundZone.cpp -o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPData.cpp -o fusion_sdk/calvin_files/data/src/CHPData.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPExpressionEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp -o fusion_sdk/calvin_files/data/src/CHPMultiDataData.o fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp: In member function 'void affymetrix_calvin_io::CHPMultiDataData::SetEntryCount(affymetrix_calvin_io::MultiDataType, int32_t, int32_t, const std::vector&, const wstring&)': fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:427:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:429:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' DataGroupHeader* dgHdr = GetDataGroupHeader(dataTypeGroupNames[dataType]); ^~~~~~~~~~~~~~~ fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp: In member function 'void affymetrix_calvin_io::CHPMultiDataData::SetEntryCount(affymetrix_calvin_io::MultiDataType, int32_t, int, int, int, const wstring&)': fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:457:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:459:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' DataGroupHeader* dgHdr = GetDataGroupHeader(dataTypeGroupNames[dataType]); ^~~~~~~~~~~~~~~ fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp: In member function 'void affymetrix_calvin_io::CHPMultiDataData::SetEntryCount(affymetrix_calvin_io::MultiDataType, int32_t, int, int, int, int, const wstring&)': fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:482:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:484:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' DataGroupHeader* dgHdr = GetDataGroupHeader(dataTypeGroupNames[dataType]); ^~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPTilingData.cpp -o fusion_sdk/calvin_files/data/src/CHPTilingData.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp -o fusion_sdk/calvin_files/data/src/CHPQuantificationData.o fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp: In member function 'void affymetrix_calvin_io::CHPQuantificationData::AddColumns(affymetrix_calvin_io::DataSetHeader&, bool)': fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp:144:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp:146:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' hdr.AddFloatColumn(QUANTIFICATION_QUANTIFICATION_NAME); ^~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp -o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp: In member function 'void affymetrix_calvin_io::CHPQuantificationDetectionData::AddColumns(affymetrix_calvin_io::DataSetHeader&, bool)': fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp:151:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp:153:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' hdr.AddFloatColumn(QUANTIFICATION_DETECTION_QUANTIFICATION_NAME); ^~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/CHPUniversalEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/ColumnInfo.cpp -o fusion_sdk/calvin_files/data/src/ColumnInfo.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/DataGroup.cpp -o fusion_sdk/calvin_files/data/src/DataGroup.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/DataGroup.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/DataGroup.h:28, from fusion_sdk/calvin_files/data/src/DataGroup.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp -o fusion_sdk/calvin_files/data/src/DataGroupHeader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/DataSet.cpp -o fusion_sdk/calvin_files/data/src/DataSet.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataSet.h:28, from fusion_sdk/calvin_files/data/src/DataSet.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/DataSet.h:25, from fusion_sdk/calvin_files/data/src/DataSet.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/DataSetHeader.cpp -o fusion_sdk/calvin_files/data/src/DataSetHeader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/FileHeader.cpp -o fusion_sdk/calvin_files/data/src/FileHeader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/GenericData.cpp -o fusion_sdk/calvin_files/data/src/GenericData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/data/src/GenericData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/data/src/GenericData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp -o fusion_sdk/calvin_files/data/src/GenericDataHeader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/exception/src/ExceptionBase.cpp -o fusion_sdk/calvin_files/exception/src/ExceptionBase.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/data/src/CELData.h:26, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.h:27, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp:22: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/data/src/CELData.h:26, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.h:27, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp:22: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/CDFFileData.h:37, from fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/file/CDFFileData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27, from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27, from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp -o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:27, from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:27, from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.h:25, from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.h:25, from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp -o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/parameter/src/ParameterException.h:24, from fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.h:27, from fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:24: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/parsers/src/CDFFileReader.h:29, from fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/parsers/src/CDFFileReader.h:29, from fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CelFileReader.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/data/src/CELData.h:26, from fusion_sdk/calvin_files/parsers/src/CelFileReader.h:27, from fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/data/src/CELData.h:26, from fusion_sdk/calvin_files/parsers/src/CelFileReader.h:27, from fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CHPFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.h:27, from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.h:27, from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.h:27, from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.h:27, from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/DataSetReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataSetReader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/FileInput.cpp -o fusion_sdk/calvin_files/parsers/src/FileInput.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/parsers/src/FileInput.h:27, from fusion_sdk/calvin_files/parsers/src/FileInput.cpp:24: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/parsers/src/FileInput.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:27, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:27, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp -o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/utils/src/checksum.h:27, from fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp:26: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/utils/src/DateTime.cpp -o fusion_sdk/calvin_files/utils/src/DateTime.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/utils/src/FileUtils.cpp -o fusion_sdk/calvin_files/utils/src/FileUtils.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Fs.h:27, from fusion_sdk/calvin_files/utils/src/FileUtils.cpp:26: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/utils/src/FileUtils.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/utils/src/StringUtils.cpp -o fusion_sdk/calvin_files/utils/src/StringUtils.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/calvin_files/utils/src/checksum.cpp -o fusion_sdk/calvin_files/utils/src/checksum.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/BPMAPFileData.cpp -o fusion_sdk/file/BPMAPFileData.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/FileIO.h:27, from fusion_sdk/file/BPMAPFileData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/file/BPMAPFileData.h:30, from fusion_sdk/file/BPMAPFileData.cpp:20: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/BPMAPFileWriter.cpp -o fusion_sdk/file/BPMAPFileWriter.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/FileIO.h:27, from fusion_sdk/file/BPMAPFileWriter.cpp:22: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/file/BPMAPFileData.h:30, from fusion_sdk/file/BPMAPFileWriter.h:26, from fusion_sdk/file/BPMAPFileWriter.cpp:20: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/CDFFileData.cpp -o fusion_sdk/file/CDFFileData.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/CDFFileData.h:37, from fusion_sdk/file/CDFFileData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/file/CDFFileData.h:31, from fusion_sdk/file/CDFFileData.cpp:21: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 fusion_sdk/file/CDFFileData.cpp: In member function 'bool affxcdf::CCDFFileData::ReadTextFormat()': fusion_sdk/file/CDFFileData.cpp:858:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] else if ( strncmp( subStr, CDFVERSION6, strlen(CDFVERSION6)) == 0) ^~ fusion_sdk/file/CDFFileData.cpp:861:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (m_Header.m_Version >= 6) ^~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/CELFileData.cpp -o fusion_sdk/file/CELFileData.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/CHPFileData.cpp -o fusion_sdk/file/CHPFileData.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/CHPFileData.h:36, from fusion_sdk/file/CHPFileData.cpp:20: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/string.h:9, from C:/rtools40/mingw64/include/c++/8.3.0/cstring:42, from fusion_sdk/file/TagValuePair.h:27, from fusion_sdk/file/CHPFileData.h:34, from fusion_sdk/file/CHPFileData.cpp:20: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/FileIO.cpp -o fusion_sdk/file/FileIO.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/FileIO.h:27, from fusion_sdk/file/FileIO.cpp:26: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/file/FileIO.cpp:23: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/file/FileIO.h:27, from fusion_sdk/file/FileWriter.h:26, from fusion_sdk/file/FileWriter.cpp:25: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/file/FileWriter.cpp:22: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/TsvFile/ClfFile.cpp -o fusion_sdk/file/TsvFile/ClfFile.o In file included from fusion_sdk/file/TsvFile/ClfFile.h:31, from fusion_sdk/file/TsvFile/ClfFile.cpp:27: fusion_sdk/file/TsvFile/TsvFile.h: In member function 'affx::TsvFile& affx::TsvFile::operator=(const affx::TsvFile&)': fusion_sdk/file/TsvFile/TsvFile.h:527:6: warning: statement has no effect [-Wunused-value] (that); /* unused var */ ~^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/TsvFile/PgfFile.cpp -o fusion_sdk/file/TsvFile/PgfFile.o In file included from fusion_sdk/file/TsvFile/PgfFile.h:32, from fusion_sdk/file/TsvFile/PgfFile.cpp:274: fusion_sdk/file/TsvFile/TsvFile.h: In member function 'affx::TsvFile& affx::TsvFile::operator=(const affx::TsvFile&)': fusion_sdk/file/TsvFile/TsvFile.h:527:6: warning: statement has no effect [-Wunused-value] (that); /* unused var */ ~^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/file/TsvFile/TsvFile.cpp -o fusion_sdk/file/TsvFile/TsvFile.o In file included from fusion_sdk/file/TsvFile/TsvFile.cpp:24: fusion_sdk/file/TsvFile/TsvFile.h: In member function 'affx::TsvFile& affx::TsvFile::operator=(const affx::TsvFile&)': fusion_sdk/file/TsvFile/TsvFile.h:527:6: warning: statement has no effect [-Wunused-value] (that); /* unused var */ ~^~~~~ fusion_sdk/file/TsvFile/TsvFile.cpp: In static member function 'static int affx::TsvFile::getLineCountInFile(const string&, bool)': fusion_sdk/file/TsvFile/TsvFile.cpp:4921:20: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] catch (exception e) { ^ fusion_sdk/file/TsvFile/TsvFile.cpp: In static member function 'static int affx::TsvFile::replaceCharInFile(const string&, char, char, bool)': fusion_sdk/file/TsvFile/TsvFile.cpp:4970:20: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] catch (exception e) { ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/AffxByteArray.cpp -o fusion_sdk/util/AffxByteArray.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Convert.h:32, from fusion_sdk/util/Err.h:34, from fusion_sdk/util/AffxString.h:29, from fusion_sdk/util/AffxByteArray.h:29, from fusion_sdk/util/AffxByteArray.cpp:27: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/string.h:9, from C:/rtools40/mingw64/include/c++/8.3.0/cstring:42, from fusion_sdk/util/AffxConv.h:33, from fusion_sdk/util/AffxByteArray.h:28, from fusion_sdk/util/AffxByteArray.cpp:27: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 fusion_sdk/util/AffxByteArray.cpp: In member function 'const AffxByteArray& AffxByteArray::operator=(const AffxByteArray&)': fusion_sdk/util/AffxByteArray.cpp:320:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (this == &ba) ^~ fusion_sdk/util/AffxByteArray.cpp:323:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' empty(); ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/AffxConv.cpp -o fusion_sdk/util/AffxConv.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Convert.h:32, from fusion_sdk/util/AffxConv.cpp:34: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/string.h:9, from C:/rtools40/mingw64/include/c++/8.3.0/cstring:42, from fusion_sdk/util/AffxConv.h:33, from fusion_sdk/util/AffxConv.cpp:32: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 fusion_sdk/util/AffxConv.cpp: In function 'std::__cxx11::string getInt(int, bool)': fusion_sdk/util/AffxConv.cpp:124:8: warning: self-comparison always evaluates to false [-Wtautological-compare] if (i != i) {return "nan";} ~~^~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/MsgStream.cpp -o fusion_sdk/util/MsgStream.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Convert.h:32, from fusion_sdk/util/Err.h:34, from fusion_sdk/util/MsgStream.cpp:33: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/string.h:9, from C:/rtools40/mingw64/include/c++/8.3.0/cstring:42, from fusion_sdk/util/MsgHandler.h:31, from fusion_sdk/util/MsgStream.h:32, from fusion_sdk/util/MsgStream.cpp:31: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/Util.cpp -o fusion_sdk/util/Util.o fusion_sdk/util/Util.cpp:220: warning: "S_IRWXG" redefined #define S_IRWXG 00070 //mask for group permissions In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:158: note: this is the location of the previous definition #define S_IRWXG (S_IRWXU >> 3) fusion_sdk/util/Util.cpp:221: warning: "S_IRGRP" redefined #define S_IRGRP 00040 //group has read permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:155: note: this is the location of the previous definition #define S_IRGRP (S_IRUSR >> 3) fusion_sdk/util/Util.cpp:222: warning: "S_IWGRP" redefined #define S_IWGRP 00020 //group has write permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:156: note: this is the location of the previous definition #define S_IWGRP (S_IWUSR >> 3) fusion_sdk/util/Util.cpp:223: warning: "S_IXGRP" redefined #define S_IXGRP 00010 //group has execute permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:157: note: this is the location of the previous definition #define S_IXGRP (S_IXUSR >> 3) fusion_sdk/util/Util.cpp:224: warning: "S_IRWXO" redefined #define S_IRWXO 00007 //mask for permissions for others (not in group) In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:163: note: this is the location of the previous definition #define S_IRWXO (S_IRWXG >> 3) fusion_sdk/util/Util.cpp:225: warning: "S_IROTH" redefined #define S_IROTH 00004 //others have read permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:160: note: this is the location of the previous definition #define S_IROTH (S_IRGRP >> 3) fusion_sdk/util/Util.cpp:226: warning: "S_IWOTH" redefined #define S_IWOTH 00002 //others have write permisson In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:161: note: this is the location of the previous definition #define S_IWOTH (S_IWGRP >> 3) fusion_sdk/util/Util.cpp:227: warning: "S_IXOTH" redefined #define S_IXOTH 00001 // others have execute permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Util.cpp:35: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:162: note: this is the location of the previous definition #define S_IXOTH (S_IXGRP >> 3) "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/Err.cpp -o fusion_sdk/util/Err.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/Fs.cpp -o fusion_sdk/util/Fs.o fusion_sdk/util/Fs.cpp:43: warning: "S_IRUSR" redefined #define S_IRUSR 00400 //owner has read permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:152: note: this is the location of the previous definition #define S_IRUSR _S_IRUSR fusion_sdk/util/Fs.cpp:44: warning: "S_IWUSR" redefined #define S_IWUSR 00200 //owner has write permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:151: note: this is the location of the previous definition #define S_IWUSR _S_IWUSR fusion_sdk/util/Fs.cpp:45: warning: "S_IXUSR" redefined #define S_IXUSR 00100 ///owner has execute permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:150: note: this is the location of the previous definition #define S_IXUSR _S_IXUSR fusion_sdk/util/Fs.cpp:46: warning: "S_IRWXG" redefined #define S_IRWXG 00070 //mask for group permissions In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:158: note: this is the location of the previous definition #define S_IRWXG (S_IRWXU >> 3) fusion_sdk/util/Fs.cpp:47: warning: "S_IRGRP" redefined #define S_IRGRP 00040 //group has read permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:155: note: this is the location of the previous definition #define S_IRGRP (S_IRUSR >> 3) fusion_sdk/util/Fs.cpp:48: warning: "S_IWGRP" redefined #define S_IWGRP 00020 //group has write permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:156: note: this is the location of the previous definition #define S_IWGRP (S_IWUSR >> 3) fusion_sdk/util/Fs.cpp:49: warning: "S_IXGRP" redefined #define S_IXGRP 00010 //group has execute permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:157: note: this is the location of the previous definition #define S_IXGRP (S_IXUSR >> 3) fusion_sdk/util/Fs.cpp:50: warning: "S_IRWXO" redefined #define S_IRWXO 00007 //mask for permissions for others (not in group) In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:163: note: this is the location of the previous definition #define S_IRWXO (S_IRWXG >> 3) fusion_sdk/util/Fs.cpp:51: warning: "S_IROTH" redefined #define S_IROTH 00004 //others have read permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:160: note: this is the location of the previous definition #define S_IROTH (S_IRGRP >> 3) fusion_sdk/util/Fs.cpp:52: warning: "S_IWOTH" redefined #define S_IWOTH 00002 //others have write permisson In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:161: note: this is the location of the previous definition #define S_IWOTH (S_IWGRP >> 3) fusion_sdk/util/Fs.cpp:53: warning: "S_IXOTH" redefined #define S_IXOTH 00001 // others have execute permission In file included from fusion_sdk/util/Fs.h:33, from fusion_sdk/util/Fs.cpp:28: C:/rtools40/mingw64/x86_64-w64-mingw32/include/sys/stat.h:162: note: this is the location of the previous definition #define S_IXOTH (S_IXGRP >> 3) fusion_sdk/util/Fs.cpp: In static member function 'static AptErr_t Fs::listDir(const string&, std::vector >&, bool)': fusion_sdk/util/Fs.cpp:1028:9: warning: unused variable 'rv' [-Wunused-variable] DWORD rv=0; ^~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/Verbose.cpp -o fusion_sdk/util/Verbose.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Fs.h:27, from fusion_sdk/util/Verbose.cpp:31: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/string.h:9, from C:/rtools40/mingw64/include/c++/8.3.0/cstring:42, from fusion_sdk/calvin_files/utils/src/StringUtils.h:27, from fusion_sdk/util/Verbose.cpp:29: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/RowFile.cpp -o fusion_sdk/util/RowFile.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Convert.h:32, from fusion_sdk/util/RowFile.cpp:30: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/string.h:9, from C:/rtools40/mingw64/include/c++/8.3.0/cstring:42, from fusion_sdk/util/RowFile.h:31, from fusion_sdk/util/RowFile.cpp:28: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/TableFile.cpp -o fusion_sdk/util/TableFile.o In file included from fusion_sdk/portability/affy-base-types.h:51, from fusion_sdk/util/Util.h:35, from fusion_sdk/util/TableFile.h:32, from fusion_sdk/util/TableFile.cpp:28: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/string.h:9, from C:/rtools40/mingw64/include/c++/8.3.0/cstring:42, from fusion_sdk/util/RowFile.h:31, from fusion_sdk/util/TableFile.h:31, from fusion_sdk/util/TableFile.cpp:28: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion_sdk/util/Convert.cpp -o fusion_sdk/util/Convert.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c R_affx_cel_parser.cpp -o R_affx_cel_parser.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27, from R_affx_cel_parser.cpp:1: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27, from R_affx_cel_parser.cpp:1: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R.h:91, from R_affx_cel_parser.cpp:9: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:55: warning: "ERROR" redefined #define ERROR ),error(R_problem_buf);} In file included from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:71, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27, from R_affx_cel_parser.cpp:1: C:/rtools40/mingw64/x86_64-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition #define ERROR 0 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c R_affx_cdf_parser.cpp -o R_affx_cdf_parser.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_parser.cpp:1: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_parser.cpp:1: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R.h:91, from R_affx_cdf_parser.cpp:9: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:55: warning: "ERROR" redefined #define ERROR ),error(R_problem_buf);} In file included from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:71, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_parser.cpp:1: C:/rtools40/mingw64/x86_64-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition #define ERROR 0 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c R_affx_cdf_extras.cpp -o R_affx_cdf_extras.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/DataGroup.h:31, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_extras.cpp:1: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_extras.cpp:1: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R.h:91, from R_affx_cdf_extras.cpp:8: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:55: warning: "ERROR" redefined #define ERROR ),error(R_problem_buf);} In file included from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:71, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28, from fusion_sdk/calvin_files/data/src/CDFData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_extras.cpp:1: C:/rtools40/mingw64/x86_64-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition #define ERROR 0 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c R_affx_bpmap_parser.cpp -o R_affx_bpmap_parser.o In file included from R_affx_bpmap_parser.cpp:4: R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/file/BPMAPFileData.h:30, from R_affx_bpmap_parser.cpp:1: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R.h:91, from R_affx_bpmap_parser.cpp:11: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:55: warning: "ERROR" redefined #define ERROR ),error(R_problem_buf);} In file included from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:71, from fusion_sdk/file/BPMAPFileData.h:30, from R_affx_bpmap_parser.cpp:1: C:/rtools40/mingw64/x86_64-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition #define ERROR 0 R_affx_bpmap_parser.cpp: In function 'SEXPREC* R_affx_get_bpmap_file(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': R_affx_bpmap_parser.cpp:482:32: warning: 'centerpos' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(centerpos)[j] = seqHit.getCenterPosition(); ~~~~~~~^~~~~~~~~~~ R_affx_bpmap_parser.cpp:479:36: warning: 'startpos' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(startpos)[j] = seqHit.getStartPosition(); ~~~~~~~^~~~~~~~~~ R_affx_bpmap_parser.cpp:485:33: warning: 'matchscore' may be used uninitialized in this function [-Wmaybe-uninitialized] REAL(matchscore)[j] = (double)seqHit.MatchScore; ~~~~^~~~~~~~~~~~ R_affx_bpmap_parser.cpp:488:32: warning: 'probelength' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(probelength)[j] = (int)seqHit.ProbeLength; ~~~~~~~^~~~~~~~~~~~~ R_affx_bpmap_parser.cpp:467:32: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(strand)[j] = (unsigned int)seqHit.TopStrand; ~~~~~~~^~~~~~~~ R_affx_bpmap_parser.cpp:475:41: warning: 'probeseq' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_STRING_ELT(probeseq, j, mkChar(cstr)); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ R_affx_bpmap_parser.cpp:502:39: warning: 'mmy' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(seqObj, kk, mmy); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ R_affx_bpmap_parser.cpp:463:32: warning: 'mmx' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(mmx)[j] = seqHit.MMX; ~~~~~~~^~~~~ R_affx_bpmap_parser.cpp:495:35: warning: 'pmy' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(seqObj, kk, pmy); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ R_affx_bpmap_parser.cpp:493:35: warning: 'pmx' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(seqObj, kk, pmx); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c R_affx_clf_pgf_parser.cpp -o R_affx_clf_pgf_parser.o In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:39, from R_affx_clf_pgf_parser.cpp:11: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:55: warning: "ERROR" redefined #define ERROR ),error(R_problem_buf);} In file included from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:71, from fusion_sdk/portability/affy-base-types.h:56, from fusion_sdk/file/TsvFile/TsvFile.h:30, from fusion_sdk/file/TsvFile/ClfFile.h:31, from R_affx_clf_pgf_parser.cpp:2: C:/rtools40/mingw64/x86_64-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition #define ERROR 0 In file included from fusion_sdk/file/TsvFile/ClfFile.h:31, from R_affx_clf_pgf_parser.cpp:2: fusion_sdk/file/TsvFile/TsvFile.h: In member function 'affx::TsvFile& affx::TsvFile::operator=(const affx::TsvFile&)': fusion_sdk/file/TsvFile/TsvFile.h:527:6: warning: statement has no effect [-Wunused-value] (that); /* unused var */ ~^~~~~ R_affx_clf_pgf_parser.cpp: In function 'SEXPREC* R_affx_get_clf_file(SEXP, SEXP, SEXP)': R_affx_clf_pgf_parser.cpp:284:21: warning: catching polymorphic type 'class Except' by value [-Wcatch-value=] } catch (Except ex) { ^~ R_affx_clf_pgf_parser.cpp: In function 'SEXPREC* R_affx_get_pgf_file(SEXP, SEXP, SEXP, SEXP)': R_affx_clf_pgf_parser.cpp:327:21: warning: catching polymorphic type 'class Except' by value [-Wcatch-value=] } catch (Except ex) { ^~ R_affx_clf_pgf_parser.cpp: In function 'void R_affx_get_body(affx::PgfFile*, SEXP, SEXP)': R_affx_clf_pgf_parser.cpp:161:23: warning: 'pindices' may be used uninitialized in this function [-Wmaybe-uninitialized] currIndex = pindices[i]; ~~~~~~~~~~^~~~~~~~~~~~~ R_affx_clf_pgf_parser.cpp:132:4: warning: 'currIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] if (nProbesets < currIndex) continue; ^~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c R_affx_chp_parser.cpp -o R_affx_chp_parser.o In file included from fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24, from fusion_sdk/calvin_files/data/src/DataException.h:27, from fusion_sdk/calvin_files/data/src/GenericData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from R_affx_chp_parser.cpp:1: ./R_affx_constants.h:17: warning: "WINVER" redefined #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ In file included from ./_mingw.h:16, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:9, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from R_affx_chp_parser.cpp:1: ./_mingw_gcc493.h:225: note: this is the location of the previous definition #define WINVER 0x0502 In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:39, from R_affx_chp_parser.cpp:21: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:55: warning: "ERROR" redefined #define ERROR ),error(R_problem_buf);} In file included from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:71, from fusion_sdk/calvin_files/data/src/GenericData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26, from R_affx_chp_parser.cpp:1: C:/rtools40/mingw64/x86_64-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition #define ERROR 0 In file included from R_affx_chp_parser.cpp:21: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h: In function 'SEXPREC* R_affx_GetCHPGenotypingResults(affymetrix_fusion_io::FusionCHPLegacyData*)': C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:142:46: warning: 'nocall' may be used uninitialized in this function [-Wmaybe-uninitialized] #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) ^ R_affx_chp_parser.cpp:318:38: note: 'nocall' was declared here SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; ^~~~~~ In file included from R_affx_chp_parser.cpp:21: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:142:46: warning: 'bb' may be used uninitialized in this function [-Wmaybe-uninitialized] #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) ^ R_affx_chp_parser.cpp:318:34: note: 'bb' was declared here SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; ^~ In file included from R_affx_chp_parser.cpp:21: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:142:46: warning: 'ab' may be used uninitialized in this function [-Wmaybe-uninitialized] #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) ^ R_affx_chp_parser.cpp:318:30: note: 'ab' was declared here SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; ^~ In file included from R_affx_chp_parser.cpp:21: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:142:46: warning: 'aa' may be used uninitialized in this function [-Wmaybe-uninitialized] #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) ^ R_affx_chp_parser.cpp:318:26: note: 'aa' was declared here SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; ^~ In file included from R_affx_chp_parser.cpp:21: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:142:46: warning: 'ras1' may be used uninitialized in this function [-Wmaybe-uninitialized] #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) ^ R_affx_chp_parser.cpp:318:14: note: 'ras1' was declared here SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; ^~~~ R_affx_chp_parser.cpp:360:11: warning: 'ras2' may be used uninitialized in this function [-Wmaybe-uninitialized] REAL(ras2)[i] = f.GetRAS2(); ~~~~^~~~~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o affxparser.dll tmp.def fusion_sdk/calvin_files/data/src/CDFData.o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o fusion_sdk/calvin_files/data/src/CELData.o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o fusion_sdk/calvin_files/data/src/CHPData.o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o fusion_sdk/calvin_files/data/src/CHPMultiDataData.o fusion_sdk/calvin_files/data/src/CHPTilingData.o fusion_sdk/calvin_files/data/src/CHPQuantificationData.o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o fusion_sdk/calvin_files/data/src/ColumnInfo.o fusion_sdk/calvin_files/data/src/DataGroup.o fusion_sdk/calvin_files/data/src/DataGroupHeader.o fusion_sdk/calvin_files/data/src/DataSet.o fusion_sdk/calvin_files/data/src/DataSetHeader.o fusion_sdk/calvin_files/data/src/FileHeader.o fusion_sdk/calvin_files/data/src/GenericData.o fusion_sdk/calvin_files/data/src/GenericDataHeader.o fusion_sdk/calvin_files/exception/src/ExceptionBase.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion_sdk/calvin_files/fusion/src/FusionCELData.o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o fusion_sdk/calvin_files/parsers/src/CelFileReader.o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataSetReader.o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o fusion_sdk/calvin_files/parsers/src/FileInput.o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o fusion_sdk/calvin_files/utils/src/DateTime.o fusion_sdk/calvin_files/utils/src/FileUtils.o fusion_sdk/calvin_files/utils/src/StringUtils.o fusion_sdk/calvin_files/utils/src/checksum.o fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o fusion_sdk/file/CHPFileData.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o fusion_sdk/file/TsvFile/ClfFile.o fusion_sdk/file/TsvFile/PgfFile.o fusion_sdk/file/TsvFile/TsvFile.o fusion_sdk/util/AffxByteArray.o fusion_sdk/util/AffxConv.o fusion_sdk/util/MsgStream.o fusion_sdk/util/Util.o fusion_sdk/util/Err.o fusion_sdk/util/Fs.o fusion_sdk/util/Verbose.o fusion_sdk/util/RowFile.o fusion_sdk/util/TableFile.o fusion_sdk/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 -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/affxparser.buildbin-libdir/affxparser/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'affxparser' as affxparser_1.64.1.zip * DONE (affxparser) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'affxparser' successfully unpacked and MD5 sums checked