[R-pkg-team] Bug#1024580: r-bioc-affxparser: FTBFS on hppa - cannot handle R_PARISC_PCREL17F

[John David Anglin]

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)
-------------- next part --------------
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 $@