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
0000231f__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:
https://buildd.debian.org/status/fetch.php?pkg=r-bioc-affxparser&arch=hppa&ver=1.70.0-1&stamp=1668959018&raw=0
The problem is a short call can't reach its long call stub. In this case,
the problem can be fixed by removing -O0 from MYCXXFLAGS. Otherwise, one
needs to add "-mlong-calls" to the CXX flags on hppa.
Regards,
Dave Anglin
-- System Information:
Debian Release: bookworm/sid
APT prefers buildd-unstable
APT policy: (500, 'buildd-unstable'), (500, 'unstable')
Architecture: hppa (parisc64)
Kernel: Linux 6.0.9 (SMP w/4 CPU threads)
Locale: LANG=C, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
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 $@
