############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL affxparser ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'affxparser' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' rm -f fusion/calvin_files/data/src/CDFData.o fusion/calvin_files/data/src/CDFProbeGroupInformation.o fusion/calvin_files/data/src/CDFProbeInformation.o fusion/calvin_files/data/src/CDFProbeSetInformation.o fusion/calvin_files/data/src/CDFQCProbeInformation.o fusion/calvin_files/data/src/CDFQCProbeSetInformation.o fusion/calvin_files/data/src/CELData.o fusion/calvin_files/data/src/CHPBackgroundZone.o fusion/calvin_files/data/src/CHPData.o fusion/calvin_files/data/src/CHPExpressionEntry.o fusion/calvin_files/data/src/CHPMultiDataData.o fusion/calvin_files/data/src/CHPTilingData.o fusion/calvin_files/data/src/CHPQuantificationData.o fusion/calvin_files/data/src/CHPQuantificationDetectionData.o fusion/calvin_files/data/src/CHPGenotypeEntry.o fusion/calvin_files/data/src/CHPUniversalEntry.o fusion/calvin_files/data/src/ColumnInfo.o fusion/calvin_files/data/src/DataGroup.o fusion/calvin_files/data/src/DataGroupHeader.o fusion/calvin_files/data/src/DataSet.o fusion/calvin_files/data/src/DataSetHeader.o fusion/calvin_files/data/src/FileHeader.o fusion/calvin_files/data/src/GenericData.o fusion/calvin_files/data/src/GenericDataHeader.o fusion/calvin_files/exception/src/ExceptionBase.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionBPMAPData.o fusion/calvin_files/fusion/src/FusionCDFData.o fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion/calvin_files/fusion/src/FusionCELData.o fusion/calvin_files/fusion/src/FusionCHPData.o fusion/calvin_files/fusion/src/FusionProbeSetResults.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionCHPLegacyData.o fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion/calvin_files/fusion/src/FusionCHPTilingData.o fusion/calvin_files/fusion/src/FusionCHPGenericData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion/calvin_files/parameter/src/ParameterNameValueType.o fusion/calvin_files/parsers/src/CDFFileReader.o fusion/calvin_files/parsers/src/CelFileReader.o fusion/calvin_files/parsers/src/CHPFileReader.o fusion/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion/calvin_files/parsers/src/CHPTilingFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion/calvin_files/parsers/src/DataGroupHeaderReader.o fusion/calvin_files/parsers/src/DataGroupReader.o fusion/calvin_files/parsers/src/DataSetHeaderReader.o fusion/calvin_files/parsers/src/DataSetReader.o fusion/calvin_files/parsers/src/FileHeaderReader.o fusion/calvin_files/parsers/src/FileInput.o fusion/calvin_files/parsers/src/GenericDataHeaderReader.o fusion/calvin_files/parsers/src/GenericFileReader.o fusion/calvin_files/utils/src/AffymetrixGuid.o fusion/calvin_files/utils/src/DateTime.o fusion/calvin_files/utils/src/FileUtils.o fusion/calvin_files/utils/src/StringUtils.o fusion/calvin_files/utils/src/checksum.o fusion/file/BPMAPFileData.o fusion/file/BPMAPFileWriter.o fusion/file/CDFFileData.o fusion/file/CELFileData.o fusion/file/CHPFileData.o fusion/file/FileIO.o fusion/file/FileWriter.o fusion/file/TsvFile/ClfFile.o fusion/file/TsvFile/PgfFile.o fusion/file/TsvFile/TsvFile.o fusion/util/AffxByteArray.o fusion/util/AffxConv.o fusion/util/MsgStream.o fusion/util/Util.o fusion/util/Err.o fusion/util/Fs.o fusion/util/Verbose.o fusion/util/RowFile.o fusion/util/TableFile.o fusion/util/Convert.o R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o R_affx_clf_pgf_parser.o R_affx_chp_parser.o 000.init.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CDFData.cpp -o fusion/calvin_files/data/src/CDFData.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/DataGroup.h:31, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion/calvin_files/data/src/CDFData.h:26, from fusion/calvin_files/data/src/CDFData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CDFProbeGroupInformation.cpp -o fusion/calvin_files/data/src/CDFProbeGroupInformation.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/DataGroup.h:31, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion/calvin_files/data/src/CDFProbeGroupInformation.h:31, from fusion/calvin_files/data/src/CDFProbeGroupInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/CDFProbeGroupInformation.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CDFProbeInformation.cpp -o fusion/calvin_files/data/src/CDFProbeInformation.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/DataSet.h:28, from fusion/calvin_files/data/src/CDFProbeInformation.h:30, from fusion/calvin_files/data/src/CDFProbeInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/CDFProbeInformation.h:27: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CDFProbeSetInformation.cpp -o fusion/calvin_files/data/src/CDFProbeSetInformation.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/DataGroup.h:31, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion/calvin_files/data/src/CDFProbeSetInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CDFQCProbeInformation.cpp -o fusion/calvin_files/data/src/CDFQCProbeInformation.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/DataSet.h:28, from fusion/calvin_files/data/src/CDFQCProbeInformation.h:27, from fusion/calvin_files/data/src/CDFQCProbeInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/DataSet.h:25: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CDFQCProbeSetInformation.cpp -o fusion/calvin_files/data/src/CDFQCProbeSetInformation.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/DataSet.h:28, from fusion/calvin_files/data/src/CDFQCProbeSetInformation.h:31, from fusion/calvin_files/data/src/CDFQCProbeSetInformation.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/CDFQCProbeSetInformation.h:25: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CELData.cpp -o fusion/calvin_files/data/src/CELData.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/data/src/CELData.h:26, from fusion/calvin_files/data/src/CELData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CHPBackgroundZone.cpp -o fusion/calvin_files/data/src/CHPBackgroundZone.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CHPData.cpp -o fusion/calvin_files/data/src/CHPData.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CHPExpressionEntry.cpp -o fusion/calvin_files/data/src/CHPExpressionEntry.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CHPMultiDataData.cpp -o fusion/calvin_files/data/src/CHPMultiDataData.o fusion/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 std::wstring&)': fusion/calvin_files/data/src/CHPMultiDataData.cpp:427:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] 427 | else | ^~~~ fusion/calvin_files/data/src/CHPMultiDataData.cpp:429:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 429 | DataGroupHeader* dgHdr = GetDataGroupHeader(dataTypeGroupNames[dataType]); | ^~~~~~~~~~~~~~~ fusion/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 std::wstring&)': fusion/calvin_files/data/src/CHPMultiDataData.cpp:457:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] 457 | else | ^~~~ fusion/calvin_files/data/src/CHPMultiDataData.cpp:459:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 459 | DataGroupHeader* dgHdr = GetDataGroupHeader(dataTypeGroupNames[dataType]); | ^~~~~~~~~~~~~~~ fusion/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 std::wstring&)': fusion/calvin_files/data/src/CHPMultiDataData.cpp:482:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] 482 | else | ^~~~ fusion/calvin_files/data/src/CHPMultiDataData.cpp:484:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 484 | DataGroupHeader* dgHdr = GetDataGroupHeader(dataTypeGroupNames[dataType]); | ^~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CHPTilingData.cpp -o fusion/calvin_files/data/src/CHPTilingData.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CHPQuantificationData.cpp -o fusion/calvin_files/data/src/CHPQuantificationData.o fusion/calvin_files/data/src/CHPQuantificationData.cpp: In member function 'void affymetrix_calvin_io::CHPQuantificationData::AddColumns(affymetrix_calvin_io::DataSetHeader&, bool)': fusion/calvin_files/data/src/CHPQuantificationData.cpp:144:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] 144 | else | ^~~~ fusion/calvin_files/data/src/CHPQuantificationData.cpp:146:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 146 | hdr.AddFloatColumn(QUANTIFICATION_QUANTIFICATION_NAME); | ^~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CHPQuantificationDetectionData.cpp -o fusion/calvin_files/data/src/CHPQuantificationDetectionData.o fusion/calvin_files/data/src/CHPQuantificationDetectionData.cpp: In member function 'void affymetrix_calvin_io::CHPQuantificationDetectionData::AddColumns(affymetrix_calvin_io::DataSetHeader&, bool)': fusion/calvin_files/data/src/CHPQuantificationDetectionData.cpp:151:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] 151 | else | ^~~~ fusion/calvin_files/data/src/CHPQuantificationDetectionData.cpp:153:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 153 | hdr.AddFloatColumn(QUANTIFICATION_DETECTION_QUANTIFICATION_NAME); | ^~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CHPGenotypeEntry.cpp -o fusion/calvin_files/data/src/CHPGenotypeEntry.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CHPUniversalEntry.cpp -o fusion/calvin_files/data/src/CHPUniversalEntry.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/ColumnInfo.cpp -o fusion/calvin_files/data/src/ColumnInfo.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/DataGroup.cpp -o fusion/calvin_files/data/src/DataGroup.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/DataGroup.h:31, from fusion/calvin_files/data/src/DataGroup.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/DataGroup.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/DataGroupHeader.cpp -o fusion/calvin_files/data/src/DataGroupHeader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/DataSet.cpp -o fusion/calvin_files/data/src/DataSet.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/DataSet.h:28, from fusion/calvin_files/data/src/DataSet.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/DataSet.h:25: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/DataSetHeader.cpp -o fusion/calvin_files/data/src/DataSetHeader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/FileHeader.cpp -o fusion/calvin_files/data/src/FileHeader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/GenericData.cpp -o fusion/calvin_files/data/src/GenericData.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/data/src/GenericData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/GenericDataHeader.cpp -o fusion/calvin_files/data/src/GenericDataHeader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/exception/src/ExceptionBase.cpp -o fusion/calvin_files/exception/src/ExceptionBase.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp -o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/data/src/CELData.h:26, from fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.h:27, from fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp:22: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp -o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/FusionBPMAPData.cpp -o fusion/calvin_files/fusion/src/FusionBPMAPData.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/FusionCDFData.cpp -o fusion/calvin_files/fusion/src/FusionCDFData.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/DataGroup.h:31, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion/calvin_files/data/src/CDFData.h:26, from fusion/calvin_files/fusion/src/FusionCDFData.h:27, from fusion/calvin_files/fusion/src/FusionCDFData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp -o fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o In file included from fusion/portability/affy-base-types.h:51, from fusion/file/CDFFileData.h:37, from fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.h:26, from fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/file/CDFFileData.h:31: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/FusionCELData.cpp -o fusion/calvin_files/fusion/src/FusionCELData.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion/calvin_files/fusion/src/FusionCELData.h:27, from fusion/calvin_files/fusion/src/FusionCELData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/FusionCHPData.cpp -o fusion/calvin_files/fusion/src/FusionCHPData.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/fusion/src/FusionCHPData.h:26, from fusion/calvin_files/fusion/src/FusionCHPData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/FusionProbeSetResults.cpp -o fusion/calvin_files/fusion/src/FusionProbeSetResults.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp -o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:27, from fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp -o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/FusionCHPLegacyData.cpp -o fusion/calvin_files/fusion/src/FusionCHPLegacyData.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/fusion/src/FusionCHPData.h:26, from fusion/calvin_files/fusion/src/FusionCHPLegacyData.h:28, from fusion/calvin_files/fusion/src/FusionCHPLegacyData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp -o fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/FusionCHPMultiDataData.cpp -o fusion/calvin_files/fusion/src/FusionCHPMultiDataData.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/FusionCHPTilingData.cpp -o fusion/calvin_files/fusion/src/FusionCHPTilingData.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/FusionCHPGenericData.cpp -o fusion/calvin_files/fusion/src/FusionCHPGenericData.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/fusion/src/FusionCHPGenericData.h:25, from fusion/calvin_files/fusion/src/FusionCHPGenericData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/FusionCHPQuantificationData.cpp -o fusion/calvin_files/fusion/src/FusionCHPQuantificationData.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.cpp -o fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parameter/src/ParameterNameValueType.cpp -o fusion/calvin_files/parameter/src/ParameterNameValueType.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/parameter/src/ParameterException.h:24, from fusion/calvin_files/parameter/src/ParameterNameValueType.h:27, from fusion/calvin_files/parameter/src/ParameterNameValueType.cpp:24: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/parameter/src/ParameterNameValueType.cpp:21: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/CDFFileReader.cpp -o fusion/calvin_files/parsers/src/CDFFileReader.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/DataGroup.h:31, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion/calvin_files/data/src/CDFData.h:26, from fusion/calvin_files/parsers/src/CDFFileReader.h:29, from fusion/calvin_files/parsers/src/CDFFileReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/CelFileReader.cpp -o fusion/calvin_files/parsers/src/CelFileReader.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/data/src/CELData.h:26, from fusion/calvin_files/parsers/src/CelFileReader.h:27, from fusion/calvin_files/parsers/src/CelFileReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/CHPFileReader.cpp -o fusion/calvin_files/parsers/src/CHPFileReader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/CHPMultiDataFileReader.cpp -o fusion/calvin_files/parsers/src/CHPMultiDataFileReader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/CHPTilingFileReader.cpp -o fusion/calvin_files/parsers/src/CHPTilingFileReader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/CHPQuantificationFileReader.cpp -o fusion/calvin_files/parsers/src/CHPQuantificationFileReader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.cpp -o fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/DataGroupHeaderReader.cpp -o fusion/calvin_files/parsers/src/DataGroupHeaderReader.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/parsers/src/DataGroupHeaderReader.h:27, from fusion/calvin_files/parsers/src/DataGroupHeaderReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/DataGroupReader.cpp -o fusion/calvin_files/parsers/src/DataGroupReader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/DataSetHeaderReader.cpp -o fusion/calvin_files/parsers/src/DataSetHeaderReader.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/parsers/src/DataSetHeaderReader.h:27, from fusion/calvin_files/parsers/src/DataSetHeaderReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/DataSetReader.cpp -o fusion/calvin_files/parsers/src/DataSetReader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/FileHeaderReader.cpp -o fusion/calvin_files/parsers/src/FileHeaderReader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/FileInput.cpp -o fusion/calvin_files/parsers/src/FileInput.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/parsers/src/FileInput.h:27, from fusion/calvin_files/parsers/src/FileInput.cpp:24: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/parsers/src/FileInput.cpp:21: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/GenericDataHeaderReader.cpp -o fusion/calvin_files/parsers/src/GenericDataHeaderReader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/parsers/src/GenericFileReader.cpp -o fusion/calvin_files/parsers/src/GenericFileReader.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/parsers/src/GenericFileReader.h:27, from fusion/calvin_files/parsers/src/GenericFileReader.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/utils/src/AffymetrixGuid.cpp -o fusion/calvin_files/utils/src/AffymetrixGuid.o In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/utils/src/checksum.h:27, from fusion/calvin_files/utils/src/AffymetrixGuid.cpp:26: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/utils/src/AffymetrixGuid.cpp:21: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/utils/src/DateTime.cpp -o fusion/calvin_files/utils/src/DateTime.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/utils/src/FileUtils.cpp -o fusion/calvin_files/utils/src/FileUtils.o In file included from fusion/portability/affy-base-types.h:51, from fusion/util/Fs.h:27, from fusion/calvin_files/utils/src/FileUtils.cpp:26: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/utils/src/FileUtils.cpp:21: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/utils/src/StringUtils.cpp -o fusion/calvin_files/utils/src/StringUtils.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/utils/src/checksum.cpp -o fusion/calvin_files/utils/src/checksum.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/file/BPMAPFileData.cpp -o fusion/file/BPMAPFileData.o In file included from fusion/portability/affy-base-types.h:51, from fusion/file/FileIO.h:27, from fusion/file/BPMAPFileData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/file/BPMAPFileData.h:30, from fusion/file/BPMAPFileData.cpp:20: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/file/BPMAPFileWriter.cpp -o fusion/file/BPMAPFileWriter.o In file included from fusion/portability/affy-base-types.h:51, from fusion/file/FileIO.h:27, from fusion/file/BPMAPFileWriter.cpp:22: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/file/BPMAPFileData.h:30, from fusion/file/BPMAPFileWriter.h:26, from fusion/file/BPMAPFileWriter.cpp:20: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/file/CDFFileData.cpp -o fusion/file/CDFFileData.o In file included from fusion/portability/affy-base-types.h:51, from fusion/file/CDFFileData.h:37, from fusion/file/CDFFileData.cpp:21: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/file/CDFFileData.h:31: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | fusion/file/CDFFileData.cpp: In member function 'bool affxcdf::CCDFFileData::ReadTextFormat()': fusion/file/CDFFileData.cpp:858:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 858 | else if ( strncmp( subStr, CDFVERSION6, strlen(CDFVERSION6)) == 0) | ^~ fusion/file/CDFFileData.cpp:861:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 861 | if (m_Header.m_Version >= 6) | ^~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/file/CELFileData.cpp -o fusion/file/CELFileData.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/file/CHPFileData.cpp -o fusion/file/CHPFileData.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/file/FileIO.cpp -o fusion/file/FileIO.o In file included from fusion/portability/affy-base-types.h:51, from fusion/file/FileIO.h:27, from fusion/file/FileIO.cpp:26: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/file/FileIO.cpp:23: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/file/FileWriter.cpp -o fusion/file/FileWriter.o In file included from fusion/portability/affy-base-types.h:51, from fusion/file/FileIO.h:27, from fusion/file/FileWriter.h:26, from fusion/file/FileWriter.cpp:25: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/file/FileWriter.cpp:22: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/file/TsvFile/ClfFile.cpp -o fusion/file/TsvFile/ClfFile.o In file included from fusion/file/TsvFile/ClfFile.h:31, from fusion/file/TsvFile/ClfFile.cpp:27: fusion/file/TsvFile/TsvFile.h: In member function 'affx::TsvFile& affx::TsvFile::operator=(const affx::TsvFile&)': fusion/file/TsvFile/TsvFile.h:527:6: warning: statement has no effect [-Wunused-value] 527 | (that); /* unused var */ | ~^~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/file/TsvFile/PgfFile.cpp -o fusion/file/TsvFile/PgfFile.o In file included from fusion/file/TsvFile/PgfFile.h:32, from fusion/file/TsvFile/PgfFile.cpp:274: fusion/file/TsvFile/TsvFile.h: In member function 'affx::TsvFile& affx::TsvFile::operator=(const affx::TsvFile&)': fusion/file/TsvFile/TsvFile.h:527:6: warning: statement has no effect [-Wunused-value] 527 | (that); /* unused var */ | ~^~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/file/TsvFile/TsvFile.cpp -o fusion/file/TsvFile/TsvFile.o In file included from fusion/file/TsvFile/TsvFile.cpp:24: fusion/file/TsvFile/TsvFile.h: In member function 'affx::TsvFile& affx::TsvFile::operator=(const affx::TsvFile&)': fusion/file/TsvFile/TsvFile.h:527:6: warning: statement has no effect [-Wunused-value] 527 | (that); /* unused var */ | ~^~~~~ fusion/file/TsvFile/TsvFile.cpp: In static member function 'static int affx::TsvFile::getLineCountInFile(const std::string&, bool)': fusion/file/TsvFile/TsvFile.cpp:4921:20: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] 4921 | catch (exception e) { | ^ fusion/file/TsvFile/TsvFile.cpp: In static member function 'static int affx::TsvFile::replaceCharInFile(const std::string&, char, char, bool)': fusion/file/TsvFile/TsvFile.cpp:4970:20: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] 4970 | catch (exception e) { | ^ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/util/AffxByteArray.cpp -o fusion/util/AffxByteArray.o fusion/util/AffxByteArray.cpp: In member function 'const AffxByteArray& AffxByteArray::operator=(const AffxByteArray&)': fusion/util/AffxByteArray.cpp:320:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 320 | if (this == &ba) | ^~ fusion/util/AffxByteArray.cpp:323:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 323 | empty(); | ^~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/util/AffxConv.cpp -o fusion/util/AffxConv.o fusion/util/AffxConv.cpp: In function 'std::string getInt(int, bool)': fusion/util/AffxConv.cpp:124:15: warning: self-comparison always evaluates to false [-Wtautological-compare] 124 | if (i != i) {return "nan";} | ~ ^~ ~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/util/MsgStream.cpp -o fusion/util/MsgStream.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/util/Util.cpp -o fusion/util/Util.o fusion/util/Util.cpp:220: warning: "S_IRWXG" redefined 220 | #define S_IRWXG 00070 //mask for group permissions | In file included from fusion/util/Fs.h:33, from fusion/util/Util.cpp:35: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:158: note: this is the location of the previous definition 158 | #define S_IRWXG (S_IRWXU >> 3) | fusion/util/Util.cpp:221: warning: "S_IRGRP" redefined 221 | #define S_IRGRP 00040 //group has read permission | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:155: note: this is the location of the previous definition 155 | #define S_IRGRP (S_IRUSR >> 3) | fusion/util/Util.cpp:222: warning: "S_IWGRP" redefined 222 | #define S_IWGRP 00020 //group has write permission | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:156: note: this is the location of the previous definition 156 | #define S_IWGRP (S_IWUSR >> 3) | fusion/util/Util.cpp:223: warning: "S_IXGRP" redefined 223 | #define S_IXGRP 00010 //group has execute permission | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:157: note: this is the location of the previous definition 157 | #define S_IXGRP (S_IXUSR >> 3) | fusion/util/Util.cpp:224: warning: "S_IRWXO" redefined 224 | #define S_IRWXO 00007 //mask for permissions for others (not in group) | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:163: note: this is the location of the previous definition 163 | #define S_IRWXO (S_IRWXG >> 3) | fusion/util/Util.cpp:225: warning: "S_IROTH" redefined 225 | #define S_IROTH 00004 //others have read permission | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:160: note: this is the location of the previous definition 160 | #define S_IROTH (S_IRGRP >> 3) | fusion/util/Util.cpp:226: warning: "S_IWOTH" redefined 226 | #define S_IWOTH 00002 //others have write permisson | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:161: note: this is the location of the previous definition 161 | #define S_IWOTH (S_IWGRP >> 3) | fusion/util/Util.cpp:227: warning: "S_IXOTH" redefined 227 | #define S_IXOTH 00001 // others have execute permission | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:162: note: this is the location of the previous definition 162 | #define S_IXOTH (S_IXGRP >> 3) | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/util/Err.cpp -o fusion/util/Err.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/util/Fs.cpp -o fusion/util/Fs.o fusion/util/Fs.cpp:43: warning: "S_IRUSR" redefined 43 | #define S_IRUSR 00400 //owner has read permission | In file included from fusion/util/Fs.h:33, from fusion/util/Fs.cpp:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:152: note: this is the location of the previous definition 152 | #define S_IRUSR _S_IRUSR | fusion/util/Fs.cpp:44: warning: "S_IWUSR" redefined 44 | #define S_IWUSR 00200 //owner has write permission | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:151: note: this is the location of the previous definition 151 | #define S_IWUSR _S_IWUSR | fusion/util/Fs.cpp:45: warning: "S_IXUSR" redefined 45 | #define S_IXUSR 00100 ///owner has execute permission | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:150: note: this is the location of the previous definition 150 | #define S_IXUSR _S_IXUSR | fusion/util/Fs.cpp:46: warning: "S_IRWXG" redefined 46 | #define S_IRWXG 00070 //mask for group permissions | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:158: note: this is the location of the previous definition 158 | #define S_IRWXG (S_IRWXU >> 3) | fusion/util/Fs.cpp:47: warning: "S_IRGRP" redefined 47 | #define S_IRGRP 00040 //group has read permission | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:155: note: this is the location of the previous definition 155 | #define S_IRGRP (S_IRUSR >> 3) | fusion/util/Fs.cpp:48: warning: "S_IWGRP" redefined 48 | #define S_IWGRP 00020 //group has write permission | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:156: note: this is the location of the previous definition 156 | #define S_IWGRP (S_IWUSR >> 3) | fusion/util/Fs.cpp:49: warning: "S_IXGRP" redefined 49 | #define S_IXGRP 00010 //group has execute permission | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:157: note: this is the location of the previous definition 157 | #define S_IXGRP (S_IXUSR >> 3) | fusion/util/Fs.cpp:50: warning: "S_IRWXO" redefined 50 | #define S_IRWXO 00007 //mask for permissions for others (not in group) | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:163: note: this is the location of the previous definition 163 | #define S_IRWXO (S_IRWXG >> 3) | fusion/util/Fs.cpp:51: warning: "S_IROTH" redefined 51 | #define S_IROTH 00004 //others have read permission | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:160: note: this is the location of the previous definition 160 | #define S_IROTH (S_IRGRP >> 3) | fusion/util/Fs.cpp:52: warning: "S_IWOTH" redefined 52 | #define S_IWOTH 00002 //others have write permisson | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:161: note: this is the location of the previous definition 161 | #define S_IWOTH (S_IWGRP >> 3) | fusion/util/Fs.cpp:53: warning: "S_IXOTH" redefined 53 | #define S_IXOTH 00001 // others have execute permission | c:\rtools43\x86_64-w64-mingw32.static.posix\include\sys\stat.h:162: note: this is the location of the previous definition 162 | #define S_IXOTH (S_IXGRP >> 3) | fusion/util/Fs.cpp: In static member function 'static AptErr_t Fs::listDir(const std::string&, std::vector >&, bool)': fusion/util/Fs.cpp:1028:9: warning: unused variable 'rv' [-Wunused-variable] 1028 | DWORD rv=0; | ^~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/util/Verbose.cpp -o fusion/util/Verbose.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/util/RowFile.cpp -o fusion/util/RowFile.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/util/TableFile.cpp -o fusion/util/TableFile.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/util/Convert.cpp -o fusion/util/Convert.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24, from fusion/calvin_files/fusion/src/FusionCELData.h:27, from R_affx_cel_parser.cpp:1: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/DataGroup.h:31, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion/calvin_files/data/src/CDFData.h:26, from fusion/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_parser.cpp:1: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/DataGroup.h:31, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:32, from fusion/calvin_files/data/src/CDFData.h:26, from fusion/calvin_files/fusion/src/FusionCDFData.h:27, from R_affx_cdf_extras.cpp:1: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/CDFProbeSetInformation.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/file/BPMAPFileData.h:30, from R_affx_bpmap_parser.cpp:1: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | 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 [-Wmaybe-uninitialized] 482 | INTEGER(centerpos)[j] = seqHit.getCenterPosition(); | ~~~~~~~^~~~~~~~~~~ R_affx_bpmap_parser.cpp:363:36: note: 'centerpos' was declared here 363 | matchscore, startpos, centerpos; | ^~~~~~~~~ R_affx_bpmap_parser.cpp:479:36: warning: 'startpos' may be used uninitialized [-Wmaybe-uninitialized] 479 | INTEGER(startpos)[j] = seqHit.getStartPosition(); | ~~~~~~~^~~~~~~~~~ R_affx_bpmap_parser.cpp:363:26: note: 'startpos' was declared here 363 | matchscore, startpos, centerpos; | ^~~~~~~~ R_affx_bpmap_parser.cpp:485:33: warning: 'matchscore' may be used uninitialized [-Wmaybe-uninitialized] 485 | REAL(matchscore)[j] = (double)seqHit.MatchScore; | ~~~~^~~~~~~~~~~~ R_affx_bpmap_parser.cpp:363:14: note: 'matchscore' was declared here 363 | matchscore, startpos, centerpos; | ^~~~~~~~~~ R_affx_bpmap_parser.cpp:488:32: warning: 'probelength' may be used uninitialized [-Wmaybe-uninitialized] 488 | INTEGER(probelength)[j] = (int)seqHit.ProbeLength; | ~~~~~~~^~~~~~~~~~~~~ R_affx_bpmap_parser.cpp:362:52: note: 'probelength' was declared here 362 | SEXP pmx, pmy, mmx, mmy, probeseq, strand, probelength, | ^~~~~~~~~~~ R_affx_bpmap_parser.cpp:467:32: warning: 'strand' may be used uninitialized [-Wmaybe-uninitialized] 467 | INTEGER(strand)[j] = (unsigned int)seqHit.TopStrand; | ~~~~~~~^~~~~~~~ R_affx_bpmap_parser.cpp:362:44: note: 'strand' was declared here 362 | SEXP pmx, pmy, mmx, mmy, probeseq, strand, probelength, | ^~~~~~ R_affx_bpmap_parser.cpp:475:41: warning: 'probeseq' may be used uninitialized [-Wmaybe-uninitialized] 475 | SET_STRING_ELT(probeseq, j, mkChar(cstr)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ R_affx_bpmap_parser.cpp:362:34: note: 'probeseq' was declared here 362 | SEXP pmx, pmy, mmx, mmy, probeseq, strand, probelength, | ^~~~~~~~ R_affx_bpmap_parser.cpp:502:39: warning: 'mmy' may be used uninitialized [-Wmaybe-uninitialized] 502 | SET_VECTOR_ELT(seqObj, kk, mmy); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ R_affx_bpmap_parser.cpp:362:29: note: 'mmy' was declared here 362 | SEXP pmx, pmy, mmx, mmy, probeseq, strand, probelength, | ^~~ R_affx_bpmap_parser.cpp:463:32: warning: 'mmx' may be used uninitialized [-Wmaybe-uninitialized] 463 | INTEGER(mmx)[j] = seqHit.MMX; | ~~~~~~~^~~~~ R_affx_bpmap_parser.cpp:362:24: note: 'mmx' was declared here 362 | SEXP pmx, pmy, mmx, mmy, probeseq, strand, probelength, | ^~~ R_affx_bpmap_parser.cpp:495:35: warning: 'pmy' may be used uninitialized [-Wmaybe-uninitialized] 495 | SET_VECTOR_ELT(seqObj, kk, pmy); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ R_affx_bpmap_parser.cpp:362:19: note: 'pmy' was declared here 362 | SEXP pmx, pmy, mmx, mmy, probeseq, strand, probelength, | ^~~ R_affx_bpmap_parser.cpp:493:35: warning: 'pmx' may be used uninitialized [-Wmaybe-uninitialized] 493 | SET_VECTOR_ELT(seqObj, kk, pmx); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ R_affx_bpmap_parser.cpp:362:14: note: 'pmx' was declared here 362 | SEXP pmx, pmy, mmx, mmy, probeseq, strand, probelength, | ^~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 fusion/file/TsvFile/ClfFile.h:31, from R_affx_clf_pgf_parser.cpp:2: fusion/file/TsvFile/TsvFile.h: In member function 'affx::TsvFile& affx::TsvFile::operator=(const affx::TsvFile&)': fusion/file/TsvFile/TsvFile.h:527:6: warning: statement has no effect [-Wunused-value] 527 | (that); /* unused var */ | ~^~~~~ R_affx_clf_pgf_parser.cpp: In function 'void R_affx_get_body(affx::PgfFile*, SEXP, SEXP)': R_affx_clf_pgf_parser.cpp:132:11: warning: 'currIndex' may be used uninitialized [-Wmaybe-uninitialized] 132 | if (nProbesets < currIndex) continue; | ^~ R_affx_clf_pgf_parser.cpp:97:23: note: 'currIndex' was declared here 97 | int i, prevIndex, currIndex, nextIndex=0, maxIndex; | ^~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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/calvin_files/portability/src/AffymetrixBaseTypes.h:27, from fusion/calvin_files/exception/src/ExceptionBase.h:24, from fusion/calvin_files/data/src/DataException.h:27, from fusion/calvin_files/data/src/GenericData.h:31, from fusion/calvin_files/fusion/src/FusionCHPData.h:26, from R_affx_chp_parser.cpp:1: ./R_affx_constants.h:17: warning: "WINVER" redefined 17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */ | In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10, from fusion/calvin_files/data/src/GenericData.h:28: c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition 182 | #define WINVER _WIN32_WINNT | In file included from R_affx_chp_parser.cpp:21: F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h: In function 'SEXPREC* R_affx_GetCHPGenotypingResults(affymetrix_fusion_io::FusionCHPLegacyData*)': F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:131:47: warning: 'nocall' may be used uninitialized [-Wmaybe-uninitialized] 131 | #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) | ^ R_affx_chp_parser.cpp:318:38: note: 'nocall' was declared here 318 | SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; | ^~~~~~ F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:131:47: warning: 'bb' may be used uninitialized [-Wmaybe-uninitialized] 131 | #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) | ^ R_affx_chp_parser.cpp:318:34: note: 'bb' was declared here 318 | SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; | ^~ F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:131:47: warning: 'ab' may be used uninitialized [-Wmaybe-uninitialized] 131 | #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) | ^ R_affx_chp_parser.cpp:318:30: note: 'ab' was declared here 318 | SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; | ^~ F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:131:47: warning: 'aa' may be used uninitialized [-Wmaybe-uninitialized] 131 | #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) | ^ R_affx_chp_parser.cpp:318:26: note: 'aa' was declared here 318 | SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; | ^~ F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:131:47: warning: 'ras1' may be used uninitialized [-Wmaybe-uninitialized] 131 | #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val) | ^ R_affx_chp_parser.cpp:318:14: note: 'ras1' was declared here 318 | 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 [-Wmaybe-uninitialized] 360 | REAL(ras2)[i] = f.GetRAS2(); | ~~~~^~~~~~ R_affx_chp_parser.cpp:318:20: note: 'ras2' was declared here 318 | SEXP rval, ras1, ras2, aa, ab, bb, nocall, call, conf, callstr, alg; | ^~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c 000.init.c -o 000.init.o g++ -std=gnu++17 -shared -s -static-libgcc -o affxparser.dll tmp.def fusion/calvin_files/data/src/CDFData.o fusion/calvin_files/data/src/CDFProbeGroupInformation.o fusion/calvin_files/data/src/CDFProbeInformation.o fusion/calvin_files/data/src/CDFProbeSetInformation.o fusion/calvin_files/data/src/CDFQCProbeInformation.o fusion/calvin_files/data/src/CDFQCProbeSetInformation.o fusion/calvin_files/data/src/CELData.o fusion/calvin_files/data/src/CHPBackgroundZone.o fusion/calvin_files/data/src/CHPData.o fusion/calvin_files/data/src/CHPExpressionEntry.o fusion/calvin_files/data/src/CHPMultiDataData.o fusion/calvin_files/data/src/CHPTilingData.o fusion/calvin_files/data/src/CHPQuantificationData.o fusion/calvin_files/data/src/CHPQuantificationDetectionData.o fusion/calvin_files/data/src/CHPGenotypeEntry.o fusion/calvin_files/data/src/CHPUniversalEntry.o fusion/calvin_files/data/src/ColumnInfo.o fusion/calvin_files/data/src/DataGroup.o fusion/calvin_files/data/src/DataGroupHeader.o fusion/calvin_files/data/src/DataSet.o fusion/calvin_files/data/src/DataSetHeader.o fusion/calvin_files/data/src/FileHeader.o fusion/calvin_files/data/src/GenericData.o fusion/calvin_files/data/src/GenericDataHeader.o fusion/calvin_files/exception/src/ExceptionBase.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionBPMAPData.o fusion/calvin_files/fusion/src/FusionCDFData.o fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion/calvin_files/fusion/src/FusionCELData.o fusion/calvin_files/fusion/src/FusionCHPData.o fusion/calvin_files/fusion/src/FusionProbeSetResults.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionCHPLegacyData.o fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion/calvin_files/fusion/src/FusionCHPTilingData.o fusion/calvin_files/fusion/src/FusionCHPGenericData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion/calvin_files/parameter/src/ParameterNameValueType.o fusion/calvin_files/parsers/src/CDFFileReader.o fusion/calvin_files/parsers/src/CelFileReader.o fusion/calvin_files/parsers/src/CHPFileReader.o fusion/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion/calvin_files/parsers/src/CHPTilingFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion/calvin_files/parsers/src/DataGroupHeaderReader.o fusion/calvin_files/parsers/src/DataGroupReader.o fusion/calvin_files/parsers/src/DataSetHeaderReader.o fusion/calvin_files/parsers/src/DataSetReader.o fusion/calvin_files/parsers/src/FileHeaderReader.o fusion/calvin_files/parsers/src/FileInput.o fusion/calvin_files/parsers/src/GenericDataHeaderReader.o fusion/calvin_files/parsers/src/GenericFileReader.o fusion/calvin_files/utils/src/AffymetrixGuid.o fusion/calvin_files/utils/src/DateTime.o fusion/calvin_files/utils/src/FileUtils.o fusion/calvin_files/utils/src/StringUtils.o fusion/calvin_files/utils/src/checksum.o fusion/file/BPMAPFileData.o fusion/file/BPMAPFileWriter.o fusion/file/CDFFileData.o fusion/file/CELFileData.o fusion/file/CHPFileData.o fusion/file/FileIO.o fusion/file/FileWriter.o fusion/file/TsvFile/ClfFile.o fusion/file/TsvFile/PgfFile.o fusion/file/TsvFile/TsvFile.o fusion/util/AffxByteArray.o fusion/util/AffxConv.o fusion/util/MsgStream.o fusion/util/Util.o fusion/util/Err.o fusion/util/Fs.o fusion/util/Verbose.o fusion/util/RowFile.o fusion/util/TableFile.o fusion/util/Convert.o R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o R_affx_clf_pgf_parser.o R_affx_chp_parser.o 000.init.o -lws2_32 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-affxparser/00new/affxparser/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (affxparser)