| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:18 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the affxparser package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 21/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| affxparser 1.71.0 (landing page) Kasper Daniel Hansen
| palomino5 | Windows Server 2022 Datacenter / x64 | ERROR | OK | ERROR | ERROR | ||||||||
| Package: affxparser |
| Version: 1.71.0 |
| Command: rm -rf affxparser.buildbin-libdir && mkdir affxparser.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=affxparser.buildbin-libdir affxparser_1.71.0.tar.gz |
| StartedAt: 2022-12-29 04:48:36 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 04:48:57 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 20.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### rm -rf affxparser.buildbin-libdir && mkdir affxparser.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=affxparser.buildbin-libdir affxparser_1.71.0.tar.gz
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* installing *source* package 'affxparser' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
rm -f 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
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wno-sign-compare -Wno-unknown-pragmas -c fusion/calvin_files/data/src/CDFData.cpp -o fusion/calvin_files/data/src/CDFData.o
In file included from fusion/calvin_files/portability/src/AffymetrixBaseTypes.h:27,
from fusion/calvin_files/exception/src/ExceptionBase.h:24,
from fusion/calvin_files/data/src/DataException.h:27,
from fusion/calvin_files/data/src/DataGroup.h:31,
from fusion/calvin_files/data/src/CDFProbeSetInformation.h:32,
from fusion/calvin_files/data/src/CDFData.h:26,
from fusion/calvin_files/data/src/CDFData.cpp:21:
./R_affx_constants.h:17: warning: "WINVER" redefined
17 | #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */
|
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:10,
from fusion/calvin_files/data/src/CDFProbeSetInformation.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\include\sdkddkver.h:182: note: this is the location of the previous definition
182 | #define WINVER _WIN32_WINNT
|
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\stdlib.h:36,
from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\mm_malloc.h:27,
from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\xmmintrin.h:34,
from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\immintrin.h:31,
from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\x86intrin.h:32,
from c:\rtools43\x86_64-w64-mingw32.static.posix\include\winnt.h:1555,
from c:\rtools43\x86_64-w64-mingw32.static.posix\include\minwindef.h:163,
from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windef.h:9,
from c:\rtools43\x86_64-w64-mingw32.static.posix\include\windows.h:69:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\cstdlib:137:11: error: 'at_quick_exit' has not been declared in '::'
137 | using ::at_quick_exit;
| ^~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\cstdlib:160:11: error: 'quick_exit' has not been declared in '::'
160 | using ::quick_exit;
| ^~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\stdlib.h:43:14: error: 'at_quick_exit' has not been declared in 'std'
43 | using std::at_quick_exit;
| ^~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\stdlib.h:46:14: error: 'quick_exit' has not been declared in 'std'
46 | using std::quick_exit;
| ^~~~~~~~~~
make: *** [Makevars.win:7: fusion/calvin_files/data/src/CDFData.o] Error 1
ERROR: compilation failed for package 'affxparser'
* removing 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/affxparser.buildbin-libdir/affxparser'