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.
