Your message dated Thu, 24 Apr 2025 12:37:17 +0000 with message-id <e1u7vpn-00hxsf...@fasolo.debian.org> and subject line Bug#1103217: fixed in r-bioc-affxparser 1.78.0-3 has caused the Debian Bug report #1103217, regarding r-bioc-affxparser: FTBFS: R_affx_cel_parser.cpp:37:33: error: expected primary-expression before 'char' to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 1103217: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1103217 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:r-bioc-affxparser Version: 1.78.0-2 Severity: serious Tags: ftbfs trixie sid Dear maintainer: During a rebuild of all packages in unstable, your package failed to build: -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --buildsystem R dh_auto_clean -O--buildsystem=R dh_autoreconf_clean -O--buildsystem=R dh_clean -O--buildsystem=R debian/rules binary dh binary --buildsystem R dh_update_autotools_config -O--buildsystem=R dh_autoreconf -O--buildsystem=R dh_auto_configure -O--buildsystem=R dh_auto_build -O--buildsystem=R dh_auto_test -O--buildsystem=R create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=R dh_prep -O--buildsystem=R debian/rules override_dh_auto_install make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_install I: R Package: affxparser Version: 1.78.0 I: Building using R version 4.5.0-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Sat, 11 Jan 2025 14:56:44 +0100 mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-affxparser/usr/lib/R/site-library R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-affxparser/usr/lib/R/site-library --clean . "--built-timestamp='Sat, 11 Jan 2025 14:56:44 +0100'" * installing *source* package âaffxparserâ ... ** this is package âaffxparserâ version â1.78.0â ** package âaffxparserâ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: âgcc (Debian 14.2.0-19) 14.2.0â using C++ compiler: âg++ (Debian 14.2.0-19) 14.2.0â make[2]: Entering directory '/<<PKGBUILDDIR>>/src' rm -f fusion/calvin_files/data/src/CDFData.o fusion/calvin_f [too-long-redacted] R_affx_chp_parser.o 000.init.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] calvin_files/data/src/CDFData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] /src/CDFProbeGroupInformation.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] /data/src/CDFProbeInformation.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] ta/src/CDFProbeSetInformation.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] ata/src/CDFQCProbeInformation.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] /src/CDFQCProbeSetInformation.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] calvin_files/data/src/CELData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] es/data/src/CHPBackgroundZone.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] calvin_files/data/src/CHPData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] s/data/src/CHPExpressionEntry.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] les/data/src/CHPMultiDataData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] _files/data/src/CHPTilingData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] ata/src/CHPQuantificationData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] HPQuantificationDetectionData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] les/data/src/CHPGenotypeEntry.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] es/data/src/CHPUniversalEntry.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] vin_files/data/src/ColumnInfo.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] lvin_files/data/src/DataGroup.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] iles/data/src/DataGroupHeader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] calvin_files/data/src/DataSet.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] _files/data/src/DataSetHeader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] vin_files/data/src/FileHeader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] in_files/data/src/GenericData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] es/data/src/GenericDataHeader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] s/exception/src/ExceptionBase.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] nAdapter/CalvinCELDataAdapter.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] nAdapter/CalvinCHPDataAdapter.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] es/fusion/src/FusionBPMAPData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] iles/fusion/src/FusionCDFData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] /src/FusionCDFQCProbeSetNames.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] iles/fusion/src/FusionCELData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] iles/fusion/src/FusionCHPData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] ion/src/FusionProbeSetResults.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] COSAdapter/GCOSCELDataAdapter.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] COSAdapter/GCOSCHPDataAdapter.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] usion/src/FusionCHPLegacyData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] rc/FusionCHPMultiDataAccessor.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] on/src/FusionCHPMultiDataData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] usion/src/FusionCHPTilingData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] sion/src/FusionCHPGenericData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] c/FusionCHPQuantificationData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] HPQuantificationDetectionData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] er/src/ParameterNameValueType.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] les/parsers/src/CDFFileReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] les/parsers/src/CelFileReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] les/parsers/src/CHPFileReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] rs/src/CHPMultiDataFileReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] rsers/src/CHPTilingFileReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] c/CHPQuantificationFileReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] tificationDetectionFileReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] ers/src/DataGroupHeaderReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] s/parsers/src/DataGroupReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] rsers/src/DataSetHeaderReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] les/parsers/src/DataSetReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] /parsers/src/FileHeaderReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] n_files/parsers/src/FileInput.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] s/src/GenericDataHeaderReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] parsers/src/GenericFileReader.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] iles/utils/src/AffymetrixGuid.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] lvin_files/utils/src/DateTime.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] vin_files/utils/src/FileUtils.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] n_files/utils/src/StringUtils.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] lvin_files/utils/src/checksum.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] -o fusion/file/BPMAPFileData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] o fusion/file/BPMAPFileWriter.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] pp -o fusion/file/CDFFileData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] pp -o fusion/file/CELFileData.o fusion/file/CELFileData.cpp: In member function âfloat affxcel::CCELFileData::GetIntensity(int)â: fusion/file/CELFileData.cpp:2409:41: warning: taking address of packed member of âaffxcel::_CELFileEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 2409 | fIntensity=MmGetFloat_I(&m_pEntries[index].Intensity); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2414:41: warning: taking address of packed member of âaffxcel::_CELFileEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 2414 | fIntensity=MmGetFloat_I(&(m_pEntries[index].Intensity)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2419:42: warning: taking address of packed member of âaffxcel::_CELFileTranscriptomeEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 2419 | fIntensity=MmGetUInt16_N(&(m_pTransciptomeEntries[index].Intensity)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp: In member function âint affxcel::CCELFileData::GetIntensities(int, std::vector<float>&)â: fusion/file/CELFileData.cpp:2445:37: warning: taking address of packed member of âaffxcel::_CELFileEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 2445 | intensities[idx]=MmGetFloat_I(&m_pEntries[idx].Intensity); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2451:37: warning: taking address of packed member of âaffxcel::_CELFileEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 2451 | intensities[idx]=MmGetFloat_I(&m_pEntries[idx].Intensity); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2457:38: warning: taking address of packed member of âaffxcel::_CELFileTranscriptomeEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 2457 | intensities[idx]=MmGetUInt16_N(&m_pTransciptomeEntries[idx].Intensity); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp: In member function âfloat affxcel::CCELFileData::GetStdv(int)â: fusion/file/CELFileData.cpp:2506:37: warning: taking address of packed member of âaffxcel::_CELFileEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 2506 | fStdev=MmGetFloat_I(&m_pEntries[index].Stdv); | ^~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2509:37: warning: taking address of packed member of âaffxcel::_CELFileEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 2509 | fStdev=MmGetFloat_I(&(m_pEntries[index].Stdv)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2512:38: warning: taking address of packed member of âaffxcel::_CELFileTranscriptomeEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 2512 | fStdev=MmGetUInt16_N(&(m_pTransciptomeEntries[index].Stdv)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp: In member function âshort int affxcel::CCELFileData::GetPixels(int)â: fusion/file/CELFileData.cpp:2551:38: warning: taking address of packed member of âaffxcel::_CELFileEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 2551 | sPixels=MmGetInt16_I(&m_pEntries[index].Pixels); | ^~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2554:38: warning: taking address of packed member of âaffxcel::_CELFileEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 2554 | sPixels=MmGetInt16_I(&m_pEntries[index].Pixels); | ^~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp: In member function âvoid affxcel::CCELFileData::SetIntensity(int, float)â: fusion/file/CELFileData.cpp:3194:30: warning: taking address of packed member of âaffxcel::_CELFileEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 3194 | MmSetFloat_I(&m_pEntries[index].Intensity,intensity); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:3199:30: warning: taking address of packed member of âaffxcel::_CELFileEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 3199 | MmSetFloat_I(&m_pEntries[index].Intensity,intensity); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:3204:31: warning: taking address of packed member of âaffxcel::_CELFileTranscriptomeEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 3204 | MmSetUInt16_N(&m_pTransciptomeEntries[index].Intensity,s); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp: In member function âvoid affxcel::CCELFileData::SetStdv(int, float)â: fusion/file/CELFileData.cpp:3251:31: warning: taking address of packed member of âaffxcel::_CELFileTranscriptomeEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 3251 | MmSetUInt16_N(&m_pTransciptomeEntries[index].Stdv,s); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:3255:30: warning: taking address of packed member of âaffxcel::_CELFileEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 3255 | MmSetFloat_I(&m_pEntries[index].Stdv,stdev); | ^~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp: In member function âvoid affxcel::CCELFileData::SetPixels(int, short int)â: fusion/file/CELFileData.cpp:3294:42: warning: taking address of packed member of âaffxcel::_CELFileEntryTypeâ may result in an unaligned pointer value [-Waddress-of-packed-member] 3294 | MmSetUInt16_I((uint16_t*)&m_pEntries[index].Pixels,(uint16_t)pixels); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] pp -o fusion/file/CHPFileData.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] eIO.cpp -o fusion/file/FileIO.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] cpp -o fusion/file/FileWriter.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] o fusion/file/TsvFile/ClfFile.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] o fusion/file/TsvFile/PgfFile.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] o fusion/file/TsvFile/TsvFile.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] -o fusion/util/AffxByteArray.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] v.cpp -o fusion/util/AffxConv.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] .cpp -o fusion/util/MsgStream.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] /Util.cpp -o fusion/util/Util.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] il/Err.cpp -o fusion/util/Err.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] util/Fs.cpp -o fusion/util/Fs.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] se.cpp -o fusion/util/Verbose.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] le.cpp -o fusion/util/RowFile.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] .cpp -o fusion/util/TableFile.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] rt.cpp -o fusion/util/Convert.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -Ifus [too-long-redacted] rser.cpp -o R_affx_cel_parser.o R_affx_cel_parser.cpp: In function âSEXPREC* R_affx_extract_cel_file_meta(affymetrix_fusion_io::FusionCELData&)â: R_affx_cel_parser.cpp:37:33: error: expected primary-expression before âcharâ 37 | cstr = Calloc(str_length+1, char); | ^~~~ R_affx_cel_parser.cpp:37:12: error: âCallocâ was not declared in this scope; did you mean âcallocâ? 37 | cstr = Calloc(str_length+1, char); | ^~~~~~ | calloc R_affx_cel_parser.cpp:41:5: error: âFreeâ was not declared in this scope; did you mean âfreeâ? 41 | Free(cstr); | ^~~~ | free R_affx_cel_parser.cpp:70:33: error: expected primary-expression before âcharâ 70 | cstr = Calloc(str_length+1, char); | ^~~~ R_affx_cel_parser.cpp:78:33: error: expected primary-expression before âcharâ 78 | cstr = Calloc(str_length+1, char); | ^~~~ R_affx_cel_parser.cpp:86:33: error: expected primary-expression before âcharâ 86 | cstr = Calloc(str_length+1, char); | ^~~~ R_affx_cel_parser.cpp:94:33: error: expected primary-expression before âcharâ 94 | cstr = Calloc(str_length+1, char); | ^~~~ R_affx_cel_parser.cpp:102:33: error: expected primary-expression before âcharâ 102 | cstr = Calloc(str_length+1, char); | ^~~~ R_affx_cel_parser.cpp:110:33: error: expected primary-expression before âcharâ 110 | cstr = Calloc(str_length+1, char); | ^~~~ make[2]: *** [Makevars:5: R_affx_cel_parser.o] Error 1 make[2]: Leaving directory '/<<PKGBUILDDIR>>/src' make[2]: Entering directory '/<<PKGBUILDDIR>>/src' make[2]: Leaving directory '/<<PKGBUILDDIR>>/src' ERROR: compilation failed for package âaffxparserâ * removing â/<<PKGBUILDDIR>>/debian/r-bioc-affxparser/usr/lib/R/site-library/affxparserâ dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-affxparser/usr/lib/R/site-library --clean . "--built-timestamp='Sat, 11 Jan 2025 14:56:44 +0100'" returned exit code 1 make[1]: *** [debian/rules:7: override_dh_auto_install] Error 25 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:4: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- The above is just how the build ends and not necessarily the most relevant part. If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202504/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you could not reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:r-bioc-affxparser, so that this is still visible in the BTS web page for this package. Thanks.
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--- Begin Message ---Source: r-bioc-affxparser Source-Version: 1.78.0-3 Done: Rebecca N. Palmer <rebecca_pal...@zoho.com> We believe that the bug you reported is fixed in the latest version of r-bioc-affxparser, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 1103...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Rebecca N. Palmer <rebecca_pal...@zoho.com> (supplier of updated r-bioc-affxparser package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 23 Apr 2025 18:57:01 +0100 Source: r-bioc-affxparser Architecture: source Version: 1.78.0-3 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t...@alioth-lists.debian.net> Changed-By: Rebecca N. Palmer <rebecca_pal...@zoho.com> Closes: 1103217 Changes: r-bioc-affxparser (1.78.0-3) unstable; urgency=medium . * Team upload. * Use R_Calloc/Realloc/Free, for R 4.5 compatibility. (Closes: #1103217) Checksums-Sha1: efeff3143d7f6555bb82fe98edabcfc46df540ce 2124 r-bioc-affxparser_1.78.0-3.dsc 94f62f14b7f4cbfbd550508937642995b28ef6f4 6532 r-bioc-affxparser_1.78.0-3.debian.tar.xz 2bbfa687fc7ed23b694e2f72596558bdfcedcfbc 11739 r-bioc-affxparser_1.78.0-3_amd64.buildinfo Checksums-Sha256: 207fbd2313c43bfb312d842b22a2b0a8317e99469feb192efbd2c03b8336a579 2124 r-bioc-affxparser_1.78.0-3.dsc f9be91aca560f9fab8bc74cf6188e379b696c7f13b4dcf05f29ad8dde52622bc 6532 r-bioc-affxparser_1.78.0-3.debian.tar.xz 21b358c8083e3db21fe0290edccc0826bff340662046ea95dd89b8d5ff3c13c4 11739 r-bioc-affxparser_1.78.0-3_amd64.buildinfo Files: 00d9e22a2811d8069ee29c762bfa9ec1 2124 gnu-r optional r-bioc-affxparser_1.78.0-3.dsc 6e7ab22d268c7d9f807867dbdff59d39 6532 gnu-r optional r-bioc-affxparser_1.78.0-3.debian.tar.xz 89aec1cca796b9dd09ba1e3c9d19143f 11739 gnu-r optional r-bioc-affxparser_1.78.0-3_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmgKKyERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFsgQ//XsWDxAOwUnbZkfHv1j4+k6AwH9zyiTnU J9Ps6FPIzTJEPjTY/pfjQuUFf6EmutZxzEURaAVFfczkh7WJ0XyiTrvTBUfnnW54 QKX2z8UxTL/tXL2c688R+tfohgTLTnlBED2ihr3LRuQepx08r9RdyQEgLnUh14U9 q+KTtC2DKentG0jvzneOh04u+uxKMYpXuSwyH9D7Yyb+e9f77z6mpW9guXsvkrWY HU3Ii2IZ0aSjZbadaUPUKz91KW0LyGpcBiOV8iBe1afirWqrQWZk7hlmdmiwk7YE 3iiGvJ03Mve5xck4K/CFgTweD636QT13NbwX4FRxaoEpsqI28sNkUNWoE8gTv68I RyLLmMHIea16OU+46+SEZ3bjyEzNKjfNMKe5fQIoOOiofMnXR+lUrdScirbptiRU Yx4pBOQ23u/XH/TIyFG6GP5zsoFAbtg5ewdelnCc1UW53A4TaIkV6J2scVEUm+Cd zsos6hj1n6/TVgqioa2i4O+jAQ1wOVYiAeROOta+0Drpb+3Ql1p22GxPVpUSaLl1 6m+pR0/jA0BSenwgmtzD0jBABNpzgwTBpjXLqhP7pg6j1EstGCAyIxm3bxxKTZCG JrsbeycKfEzAEuVLpD0E4b+KoCpuBzRSesXCyDEOgQ3TlKQJ75pXEHKU+1mnzQcZ urepBxBZsSI= =w929 -----END PGP SIGNATURE-----
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