Bug#1024580: r-bioc-affxparser: FTBFS on hppa - cannot handle R_PARISC_PCREL17F
Hi John, Am Mon, Nov 21, 2022 at 06:27:59PM + schrieb John David Anglin: > Source: r-bioc-affxparser > Version: 1.70.0-1 > Severity: normal > Tags: ftbfs patch > ... > Index: r-bioc-affxparser-1.68.1/src/Makevars > === > --- r-bioc-affxparser-1.68.1.orig/src/Makevars > +++ r-bioc-affxparser-1.68.1/src/Makevars > @@ -1,5 +1,5 @@ > ## -Wno-unused-private-field gives notes/errors with some compiler > -MYCXXFLAGS = -Wno-sign-compare -O0 > +MYCXXFLAGS = -Wno-sign-compare > > %.o: %.cpp > $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) $(MYCXXFLAGS) -c $< -o $@ Thanks a lot for the patch. I admit I think this is only half of the solution. It deactivated optimisation for all architectures which means a diversion from -O2 default. If there is no better solution this patch (which I added in Git) should be applied only for hppa. Kind regards Andreas. -- http://fam-tille.de
Bug#1024580: r-bioc-affxparser: FTBFS on hppa - cannot handle R_PARISC_PCREL17F
Source: r-bioc-affxparser Version: 1.70.0-1 Severity: normal Tags: ftbfs patch Dear Maintainer, Build fails here: g++ -std=gnu++14 -shared -L/usr/lib/R/lib -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 000.init.o -L/usr/lib/R/lib -lR /usr/bin/ld: fusion/calvin_files/data/src/CHPQuantificationData.o(.text._ZN20affymetrix_calvin_io21CHPQuantificationData10AddColumnsERNS_13DataSetHeaderEb+0x6c): cannot reach 231f__ZN20affymetrix_calvin_io13DataSetHeader14AddAsciiColumnERKNSt7__cxx1112basic_stringIwSt11char_traitsIwESaIwEEEi+0, recompile with -ffunction-sections /usr/bin/ld: fusion/calvin_files/data/src/CHPQuantificationData.o(.text._ZN20affymetrix_calvin_io21CHPQuantificationData10AddColumnsERNS_13DataSetHeaderEb+0x6c): cannot handle R_PARISC_PCREL17F for _ZN20affymetrix_calvin_io13DataSetHeader14AddAsciiColumnERKNSt7__cxx1112basic_stringIwSt11char_traitsIwESaIwEEEi /usr/bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status make[2]: *** [/usr/share/R/share/make/shlib.mk:10: affxparser.so] Error 1 Full log is here:
