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HenrikBengtsson / affxparser

🔬 R package: This is the Bioconductor devel version of the affxparser package.
http://bioconductor.org/packages/devel/bioc/html/affxparser.html
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Build error #36

Closed starsareintherose closed 2 years ago

starsareintherose commented 2 years ago 
* installing *source* package ‘affxparser’ ...
** using staged installation
** libs
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
g++ -std=gnu++14 -I"/usr/include/R/" -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_  -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto  -Wno-sign-compare -O0 -c R_affx_cel_parser.cpp -o R_affx_cel_parser.o
g++ -std=gnu++14 -I"/usr/include/R/" -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_  -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto  -Wno-sign-compare -O0 -c R_affx_cdf_parser.cpp -o R_affx_cdf_parser.o
In file included from /usr/include/sys/types.h:25,
                 from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:81,
                 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:
/usr/include/features.h:412:4: warning: #warning _FORTIFY_SOURCE requires compiling with optimization (-O) [-Wcpp]
  412 | #  warning _FORTIFY_SOURCE requires compiling with optimization (-O)
      |    ^~~~~~~
In file included from /usr/include/sys/types.h:25,
                 from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:81,
                 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:
/usr/include/features.h:412:4: warning: #warning _FORTIFY_SOURCE requires compiling with optimization (-O) [-Wcpp]
  412 | #  warning _FORTIFY_SOURCE requires compiling with optimization (-O)
      |    ^~~~~~~
g++ -std=gnu++14 -I"/usr/include/R/" -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_  -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto  -Wno-sign-compare -O0 -c R_affx_cdf_extras.cpp -o R_affx_cdf_extras.o
In file included from /usr/include/sys/types.h:25,
                 from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:81,
                 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:
/usr/include/features.h:412:4: warning: #warning _FORTIFY_SOURCE requires compiling with optimization (-O) [-Wcpp]
  412 | #  warning _FORTIFY_SOURCE requires compiling with optimization (-O)
      |    ^~~~~~~
g++ -std=gnu++14 -I"/usr/include/R/" -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_  -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto  -Wno-sign-compare -O0 -c R_affx_bpmap_parser.cpp -o R_affx_bpmap_parser.o
In file included from /usr/include/c++/11.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39,
                 from /usr/include/c++/11.2.0/x86_64-pc-linux-gnu/bits/c++config.h:586,
                 from /usr/include/c++/11.2.0/cstring:41,
                 from fusion/file/TagValuePair.h:27,
                 from fusion/file/BPMAPFileData.h:35,
                 from R_affx_bpmap_parser.cpp:1:
/usr/include/features.h:412:4: warning: #warning _FORTIFY_SOURCE requires compiling with optimization (-O) [-Wcpp]
  412 | #  warning _FORTIFY_SOURCE requires compiling with optimization (-O)
      |    ^~~~~~~
g++ -std=gnu++14 -I"/usr/include/R/" -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_  -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto  -Wno-sign-compare -O0 -c R_affx_clf_pgf_parser.cpp -o R_affx_clf_pgf_parser.o
In file included from /usr/include/c++/11.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39,
                 from /usr/include/c++/11.2.0/x86_64-pc-linux-gnu/bits/c++config.h:586,
                 from /usr/include/c++/11.2.0/utility:68,
                 from /usr/include/c++/11.2.0/algorithm:60,
                 from fusion/portability/affy-base-types.h:60,
                 from fusion/file/TsvFile/TsvFile.h:30,
                 from fusion/file/TsvFile/ClfFile.h:31,
                 from R_affx_clf_pgf_parser.cpp:2:
/usr/include/features.h:412:4: warning: #warning _FORTIFY_SOURCE requires compiling with optimization (-O) [-Wcpp]
  412 | #  warning _FORTIFY_SOURCE requires compiling with optimization (-O)
      |    ^~~~~~~
g++ -std=gnu++14 -I"/usr/include/R/" -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_  -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto  -Wno-sign-compare -O0 -c R_affx_chp_parser.cpp -o R_affx_chp_parser.o
In file included from /usr/include/sys/types.h:25,
                 from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:81,
                 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:
/usr/include/features.h:412:4: warning: #warning _FORTIFY_SOURCE requires compiling with optimization (-O) [-Wcpp]
  412 | #  warning _FORTIFY_SOURCE requires compiling with optimization (-O)
      |    ^~~~~~~
g++ -std=gnu++14 -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto -o affxparser.so 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 -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CDFData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CDFProbeGroupInformation.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CDFProbeInformation.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CDFProbeSetInformation.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CDFQCProbeInformation.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CDFQCProbeSetInformation.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CELData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CHPBackgroundZone.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CHPData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CHPExpressionEntry.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CHPMultiDataData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CHPTilingData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CHPQuantificationData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CHPQuantificationDetectionData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CHPGenotypeEntry.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/CHPUniversalEntry.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/ColumnInfo.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/DataGroup.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/DataGroupHeader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/DataSet.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/DataSetHeader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/FileHeader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/GenericData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/data/src/GenericDataHeader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/exception/src/ExceptionBase.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/FusionBPMAPData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/FusionCDFData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/FusionCELData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/FusionCHPData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/FusionProbeSetResults.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/FusionCHPLegacyData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/FusionCHPMultiDataData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/FusionCHPTilingData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/FusionCHPGenericData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/FusionCHPQuantificationData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parameter/src/ParameterNameValueType.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/CDFFileReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/CelFileReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/CHPFileReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/CHPMultiDataFileReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/CHPTilingFileReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/CHPQuantificationFileReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/DataGroupHeaderReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/DataGroupReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/DataSetHeaderReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/DataSetReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/FileHeaderReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/FileInput.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/GenericDataHeaderReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/parsers/src/GenericFileReader.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/utils/src/AffymetrixGuid.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/utils/src/DateTime.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/utils/src/FileUtils.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/utils/src/StringUtils.o: No such file or directory
/usr/bin/ld: cannot find fusion/calvin_files/utils/src/checksum.o: No such file or directory
/usr/bin/ld: cannot find fusion/file/BPMAPFileData.o: No such file or directory
/usr/bin/ld: cannot find fusion/file/BPMAPFileWriter.o: No such file or directory
/usr/bin/ld: cannot find fusion/file/CDFFileData.o: No such file or directory
/usr/bin/ld: cannot find fusion/file/CELFileData.o: No such file or directory
/usr/bin/ld: cannot find fusion/file/CHPFileData.o: No such file or directory
/usr/bin/ld: cannot find fusion/file/FileIO.o: No such file or directory
/usr/bin/ld: cannot find fusion/file/FileWriter.o: No such file or directory
/usr/bin/ld: cannot find fusion/file/TsvFile/ClfFile.o: No such file or directory
/usr/bin/ld: cannot find fusion/file/TsvFile/PgfFile.o: No such file or directory
/usr/bin/ld: cannot find fusion/file/TsvFile/TsvFile.o: No such file or directory
/usr/bin/ld: cannot find fusion/util/AffxByteArray.o: No such file or directory
/usr/bin/ld: cannot find fusion/util/AffxConv.o: No such file or directory
/usr/bin/ld: cannot find fusion/util/MsgStream.o: No such file or directory
/usr/bin/ld: cannot find fusion/util/Util.o: No such file or directory
/usr/bin/ld: cannot find fusion/util/Err.o: No such file or directory
/usr/bin/ld: cannot find fusion/util/Fs.o: No such file or directory
/usr/bin/ld: cannot find fusion/util/Verbose.o: No such file or directory
/usr/bin/ld: cannot find fusion/util/RowFile.o: No such file or directory
/usr/bin/ld: cannot find fusion/util/TableFile.o: No such file or directory
/usr/bin/ld: cannot find fusion/util/Convert.o: No such file or directory
HenrikBengtsson commented 2 years ago

Thanks for reporting. Unfortunately, I cannot reproduce this on CentOS 7 with R 4.1.2 and gcc 11.2.1.

Your output looks very short. Specifically, it only shows that a handful of g++ compilations, but there should be many more than that (see below), so check that.

My details

I've tested with:

$ gcc --version
gcc (GCC) 11.2.1 20210728 (Red Hat 11.2.1-1)
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

and

$ R CMD config --all
CC = gcc
CFLAGS = -g -O2
CPICFLAGS = -fpic
CPPFLAGS = -I/usr/local/include
CXX = g++ -std=gnu++14
CXXFLAGS = -g -O2
CXXPICFLAGS = -fpic
CXX11STD = -std=gnu++11
CXX11FLAGS = -g -O2
CXX11PICFLAGS = -fpic
CXX14 = g++
CXX14STD = -std=gnu++14
CXX14FLAGS = -g -O2
CXX14PICFLAGS = -fpic
CXX17 = g++
CXX17STD = -std=gnu++17
CXX17FLAGS = -g -O2
CXX17PICFLAGS = -fpic
CXX20 = g++
CXX20STD = -std=gnu++2a
CXX20FLAGS = -g -O2
CXX20PICFLAGS = -fpic
DYLIB_EXT = .so
DYLIB_LD = gcc
DYLIB_LDFLAGS = -shared -fopenmp
FC = gfortran
FFLAGS = -g -O2
FPICFLAGS = -fpic
FLIBS = -lgfortran -lm -lquadmath
FCFLAGS = -g -O2
SAFE_FFLAGS = -g -O2 -msse2 -mfpmath=sse
OBJC =
OBJCFLAGS =
JAVA = /usr/lib/jvm/java-1.8.0/jre/bin/java
JAVAC = /usr/lib/jvm/java-1.8.0/bin/javac
JAVAH = /usr/lib/jvm/java-1.8.0/bin/javah
JAR = /usr/lib/jvm/java-1.8.0/bin/jar
JAVA_HOME = /usr/lib/jvm/java-1.8.0
JAVA_LIBS = -L/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server -ljvm
JAVA_CPPFLAGS = -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux
LDFLAGS = -L/usr/local/lib64
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = g++ -std=gnu++14
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX11LD = g++ -std=gnu++11
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LD = g++ -std=gnu++14
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LD = g++ -std=gnu++17
SHLIB_CXX17LDFLAGS = -shared
SHLIB_CXX20LD = g++ -std=gnu++2a
SHLIB_CXX20LDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FFLAGS =
SHLIB_LD = gcc
SHLIB_LDFLAGS = -shared
TCLTK_CPPFLAGS = -I/usr/include -I/usr/include
TCLTK_LIBS = -L/usr/lib64 -ltcl8.5 -L/usr/lib64 -ltk8.5 -lX11
BLAS_LIBS = -L/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/lib -lRblas
LAPACK_LIBS = -L/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/lib -lRlapack
MAKE = make
LIBnn = lib64
AR = ar
NM = /opt/rh/devtoolset-8/root/usr/bin/nm -B
RANLIB = ranlib
LTO =
LTO_FC =
LTO_LD =

## The following variables are defunct
CPP CXXCPP
$ wget https://www.bioconductor.org/packages/release/bioc/src/contrib/affxparser_1.66.0.tar.gz
$ R CMD INSTALL affxparser_1.66.0.tar.gz
* installing to library ‘/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8’
* installing *source* package ‘affxparser’ ...
** using staged installation
** libs
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
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFData.cpp -o fusion/calvin_files/data/src/CDFData.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFProbeGroupInformation.cpp -o fusion/calvin_files/data/src/CDFProbeGroupInformation.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFProbeInformation.cpp -o fusion/calvin_files/data/src/CDFProbeInformation.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFProbeSetInformation.cpp -o fusion/calvin_files/data/src/CDFProbeSetInformation.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFQCProbeInformation.cpp -o fusion/calvin_files/data/src/CDFQCProbeInformation.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFQCProbeSetInformation.cpp -o fusion/calvin_files/data/src/CDFQCProbeSetInformation.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CELData.cpp -o fusion/calvin_files/data/src/CELData.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPBackgroundZone.cpp -o fusion/calvin_files/data/src/CHPBackgroundZone.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPData.cpp -o fusion/calvin_files/data/src/CHPData.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPExpressionEntry.cpp -o fusion/calvin_files/data/src/CHPExpressionEntry.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPMultiDataData.cpp -o fusion/calvin_files/data/src/CHPMultiDataData.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPTilingData.cpp -o fusion/calvin_files/data/src/CHPTilingData.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPQuantificationData.cpp -o fusion/calvin_files/data/src/CHPQuantificationData.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPQuantificationDetectionData.cpp -o fusion/calvin_files/data/src/CHPQuantificationDetectionData.o[ ... many more g++ calls ... ]

g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/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_  -I/usr/local/include   -fpic  -g -O2  -Wno-sign-compare -O0 -c R_affx_chp_parser.cpp -o R_affx_chp_parser.o
g++ -std=gnu++14 -shared -L/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/lib -L/usr/local/lib64 -o affxparser.so 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 -L/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/lib -lR
installing to /c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/00LOCK-affxparser/00new/affxparser/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (affxparser)

Note also that I do not get those:

/usr/include/features.h:412:4: warning: #warning _FORTIFY_SOURCE requires compiling with optimization (-O) [-Wcpp]
  412 | #  warning _FORTIFY_SOURCE requires compiling with optimization (-O)
      |    ^~~~~~~

warnings. Don't think it matters because they're not error, but who know ¯_(ツ)_/¯

starsareintherose commented 2 years ago

I don't know why it rm firstly, and then report it can't find this files and also it should use the files user /usr/include but they don'.t

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
g++ -std=gnu++14 -I"/usr/include/R/" -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_  -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto  -Wno-sign-compare -O0 -c R_affx_cel_parser.cpp -o R_affx_cel_parser.o
g++ -std=gnu++14 -I"/usr/include/R/" -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_  -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto  -Wno-sign-compare -O0 -c R_affx_cdf_parser.cpp -o R_affx_cdf_parser.o

This is my R configure

CC = gcc
CFLAGS = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto
CPICFLAGS = -fpic
CPPFLAGS = -I/usr/local/include
CXX = g++ -std=gnu++14
CXXFLAGS = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto
CXXPICFLAGS = -fpic
CXX11 = g++
CXX11STD = -std=gnu++11
CXX11FLAGS = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto
CXX11PICFLAGS = -fpic
CXX14 = g++
CXX14STD = -std=gnu++14
CXX14FLAGS = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto
CXX14PICFLAGS = -fpic
CXX17 = g++
CXX17STD = -std=gnu++17
CXX17FLAGS = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto
CXX17PICFLAGS = -fpic
CXX20 = g++
CXX20STD = -std=gnu++20
CXX20FLAGS = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto
CXX20PICFLAGS = -fpic
DYLIB_EXT = .so
DYLIB_LD = gcc
DYLIB_LDFLAGS = -shared -fopenmp
FC = gfortran
FFLAGS = -g -O2
FPICFLAGS = -fpic
FLIBS = -lgfortran -lm -lquadmath
FCFLAGS = -g -O2
SAFE_FFLAGS = -g -O2 -msse2 -mfpmath=sse
OBJC =
OBJCFLAGS =
JAVA = /usr/bin/java
JAVAC = /usr/bin/javac
JAVAH =
JAR = /usr/bin/jar
JAVA_HOME = /usr/lib/jvm/java-17-openjdk
JAVA_LIBS = -L/usr/lib/jvm/java-17-openjdk/lib/server -ljvm
JAVA_CPPFLAGS = -I/usr/lib/jvm/java-17-openjdk/include -I/usr/lib/jvm/java-17-openjdk/include/linux
LDFLAGS = -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = g++ -std=gnu++14
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX11LD = g++ -std=gnu++11
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LD = g++ -std=gnu++14
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LD = g++ -std=gnu++17
SHLIB_CXX17LDFLAGS = -shared
SHLIB_CXX20LD = g++ -std=gnu++20
SHLIB_CXX20LDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FFLAGS =
SHLIB_LD = gcc
SHLIB_LDFLAGS = -shared
TCLTK_CPPFLAGS = -I/usr/include -I/usr/include
TCLTK_LIBS = -L/usr/lib -ltcl8.6 -L/usr/lib -ltk8.6 -lX11 -lXss -lXext
BLAS_LIBS = -lblas
LAPACK_LIBS = -llapack
MAKE = make
LIBnn = lib
AR = ar
NM = /usr/bin/nm -B
RANLIB = ranlib
LTO =
LTO_FC =
LTO_LD =

## The following variables are defunct
CPP CXXCPP
HenrikBengtsson commented 2 years ago

The rm is done by the package installation Makevars. It's by design and is not the cause of your problems.

In the second round, you didn't get those warnings. It looks to me that you're doing different things each time(?). Like I did, please share the command you call to install the package.

starsareintherose commented 2 years ago

Hello, I use ArchLinux PKGBUILD here and depedncies use this in a clean chroot to build this.

starsareintherose commented 2 years ago

In the second round, you didn't get those warnings. It looks to me that you're doing different things each time(?)

I just put part of the log to show it.

HenrikBengtsson commented 2 years ago

You don't need to use https://github.com/HenrikBengtsson/Affx-Fusion-SDK - that's just me archiving that source code for the world in case it's no longer available from Affymetrix. The affxparser package comes with all source code files required. Make sure to try without Affx-Fusion-SDK on any paths that might conflict with the compiler. I would also try to install it manually as I did and not via a package manager. Also, verify that you can install other packages from C source, e.g. digest, matrixStats, ...

FYI, since the start 2005/2006, I've never seen this type of problem reported, plus the fact that it only attempts to compile a small set of the cpp files, makes me believe there's something with your setup. I would be surprised that we haven't had a single ArchLinux user during all these years, so I don't think it's ArchLinux (but that's just a guess).

starsareintherose commented 2 years ago

I can successfully build digest, matrixStats, almost all Bioconductor packages, I can build successfully.

I remove the affx sdk, and it reports the same error

starsareintherose commented 2 years ago

Could I know what depends it should be with? Because I found this situation only exists in a clean chroot enviroment.

starsareintherose commented 2 years ago

in the clean chroot, after it is finished, it uses ld to test, but in a normal environment, it directly enters the packaging.

starsareintherose commented 2 years ago

it would be a lilac issue

HenrikBengtsson commented 2 years ago

Could I know what depends it should be with? Because I found this situation only exists in a clean chroot enviroment.

Ok that's probable key to the problem. Whenever report issues (here and any other R projects), please always try with R --vanilla and standard approaches first. That'll help rule out lots of things, and it increases the chances for someone else to be able to help out.

FWIW, on Ubuntu 18.04, the libraries that affxparser depends on are:

$ ldd ~/R/x86_64-pc-linux-gnu-library/4.1/affxparser/libs/affxparser.so 
    linux-vdso.so.1 (0x00007ffdaa3c3000)
    libR.so => /usr/lib/libR.so (0x00007f4d0c425000)
    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f4d0c09c000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f4d0bcfe000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f4d0bae6000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f4d0b6f5000)
    libblas.so.3 => /usr/lib/x86_64-linux-gnu/libblas.so.3 (0x00007f4d0b488000)
    libreadline.so.7 => /lib/x86_64-linux-gnu/libreadline.so.7 (0x00007f4d0b23f000)
    libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f4d0afcd000)
    liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f4d0ada7000)
    libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007f4d0ab97000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f4d0a97a000)
    librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f4d0a772000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f4d0a56e000)
    libicuuc.so.60 => /usr/lib/x86_64-linux-gnu/libicuuc.so.60 (0x00007f4d0a1b6000)
    libicui18n.so.60 => /usr/lib/x86_64-linux-gnu/libicui18n.so.60 (0x00007f4d09d15000)
    libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f4d09ae6000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f4d098c7000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f4d0cfb5000)
    libtinfo.so.5 => /lib/x86_64-linux-gnu/libtinfo.so.5 (0x00007f4d0969d000)
    libicudata.so.60 => /usr/lib/x86_64-linux-gnu/libicudata.so.60 (0x00007f4d07af4000)

I'm not sure if all those are considered standard dependencies in R, or if some of them should to be mentioned in SystemRequirements of the affxparser's DESCRIPTION file.