[BioC] errors with attempted installation of package affxparser
Kasper Daniel Hansen
khansen at stat.berkeley.edu
Thu Aug 28 18:35:19 CEST 2008
Hi Mark
See below for a comment, I think that (despite your attempts to work
work around this) that you are still using GCC 4.3
I will report to the main list when it works on GCC 4.3
Kasper
On Aug 28, 2008, at 9:21 AM, Mark Kimpel wrote:
> I'm not sure what you mean by the entire compilation command, but
> below is my install packages command, with flags for gcc-4.2 and the
> compile output. BTW, I just tried installing on a remote Linux
> cluster and it installs just fine
>
> mkimpel at Quarry: ~> gcc --version
> gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-10)
>
>
> Here you go, please let me know if I can provide any other useful
> information. For now, I will just use the remote cluster for what I
> need. Will you submit a post when the problem is fixed? Mark
>
>> repos <- biocReposList()
>> install.packages("affxparser", repos=repos,configure.args =
>> c('CC=/usr/bin/gcc-4.2', 'CXX=/usr/bin/g++-4.2'))
> Warning in install.packages("affxparser", repos = repos,
> configure.args = c("CC=/usr/bin/gcc-4.2", :
> argument 'lib' is missing: using '/home/mkimpel/R_HOME/site-
> library-2.8.0'
> trying URL 'http://bioconductor.org/packages/2.3/bioc/src/contrib/affxparser_1.13.7.tar.gz'
> Content type 'application/x-gzip' length 633900 bytes (619 Kb)
> opened URL
> ==================================================
> downloaded 619 Kb
>
> * Installing *source* package 'affxparser' ...
> ** libs
> rm -f fusion_sdk/calvin_files/data/src/CDFData.o
> fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o
> fusion_sdk/calvin_files/data/src/CDFProbeInformation.o
> fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o
> fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o
> fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o
> fusion_sdk/calvin_files/data/src/CELData.o
> fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o
> fusion_sdk/calvin_files/data/src/CHPData.o
> fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o
> fusion_sdk/calvin_files/data/src/CHPMultiDataData.o
> fusion_sdk/calvin_files/data/src/CHPTilingData.o
> fusion_sdk/calvin_files/data/src/CHPQuantificationData.o
> fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o
> fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o
> fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o
> fusion_sdk/calvin_files/data/src/DataGroup.o
> fusion_sdk/calvin_files/data/src/DataGroupHeader.o
> fusion_sdk/calvin_files/data/src/DataSet.o
> fusion_sdk/calvin_files/data/src/DataSetHeader.o
> fusion_sdk/calvin_files/data/src/FileHeader.o
> fusion_sdk/calvin_files/data/src/GenericData.o
> fusion_sdk/calvin_files/data/src/GenericDataHeader.o
> fusion_sdk/calvin_files/exception/src/ExceptionBase.o
> fusion_sdk/calvin_files/fusion/src/CalvinAdapter/
> CalvinCELDataAdapter.o
> fusion_sdk/calvin_files/fusion/src/CalvinAdapter/
> CalvinCHPDataAdapter.o
> fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o
> fusion_sdk/calvin_files/fusion/src/FusionCDFData.o
> fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o
> fusion_sdk/calvin_files/fusion/src/FusionCELData.o
> fusion_sdk/calvin_files/fusion/src/FusionCHPData.o
> fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o
> fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o
> fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o
> fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o
> fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o
> fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o
> fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o
> fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o
> fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o
> fusion_sdk/calvin_files/fusion/src/
> FusionCHPQuantificationDetectionData.o
> fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o
> fusion_sdk/calvin_files/parsers/src/CDFFileReader.o
> fusion_sdk/calvin_files/parsers/src/CelFileReader.o
> fusion_sdk/calvin_files/parsers/src/CHPFileReader.o
> fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o
> fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o
> fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o
> fusion_sdk/calvin_files/parsers/src/
> CHPQuantificationDetectionFileReader.o
> fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o
> fusion_sdk/calvin_files/parsers/src/DataGroupReader.o
> fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o
> fusion_sdk/calvin_files/parsers/src/DataSetReader.o
> fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o
> fusion_sdk/calvin_files/parsers/src/FileInput.o
> fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o
> fusion_sdk/calvin_files/parsers/src/GenericFileReader.o
> fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o
> fusion_sdk/calvin_files/utils/src/DateTime.o
> fusion_sdk/calvin_files/utils/src/FileUtils.o
> fusion_sdk/calvin_files/utils/src/StringUtils.o
> fusion_sdk/calvin_files/utils/src/checksum.o
> fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o
> fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o
> fusion_sdk/file/CHPFileData.o fusion_sdk/file/FileIO.o
> fusion_sdk/file/FileWriter.o fusion_sdk/file/TsvFile/TsvFile.o
> fusion_sdk/util/MsgStream.o fusion_sdk/util/Util.o
> fusion_sdk/util/RowFile.o fusion_sdk/util/TableFile.o
> fusion_sdk/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
> g++ -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include -imacros
Here you can see that the file is being compiled with the command "g+
+", which I guess links to GCC 4.3 (just do
# g++ --version
on the command line)
I was not aware that you can switch compilers by the config-args
argument, and it certainly does not seem to work I would say.
Kasper
>
> R_affx_constants.h -Ifusion_sdk/calvin_files/array/src
> -Ifusion_sdk/calvin_files/data/src
> -Ifusion_sdk/calvin_files/exception/src
> -Ifusion_sdk/calvin_files/fusion/src
> -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter
> -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter
> -Ifusion_sdk/calvin_files/parameter/src
> -Ifusion_sdk/calvin_files/parsers/src
> -Ifusion_sdk/calvin_files/portability/src
> -Ifusion_sdk/calvin_files/template/src
> -Ifusion_sdk/calvin_files/utils/src
> -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file
> -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util
> -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2
> -O0 -c fusion_sdk/calvin_files/data/src/CDFData.cpp -o
> fusion_sdk/calvin_files/data/src/CDFData.o
> g++ -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include -imacros
> R_affx_constants.h -Ifusion_sdk/calvin_files/array/src
> -Ifusion_sdk/calvin_files/data/src
> -Ifusion_sdk/calvin_files/exception/src
> -Ifusion_sdk/calvin_files/fusion/src
> -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter
> -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter
> -Ifusion_sdk/calvin_files/parameter/src
> -Ifusion_sdk/calvin_files/parsers/src
> -Ifusion_sdk/calvin_files/portability/src
> -Ifusion_sdk/calvin_files/template/src
> -Ifusion_sdk/calvin_files/utils/src
> -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file
> -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util
> -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2
> -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp
> -o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o
> g++ -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include -imacros
> R_affx_constants.h -Ifusion_sdk/calvin_files/array/src
> -Ifusion_sdk/calvin_files/data/src
> -Ifusion_sdk/calvin_files/exception/src
> -Ifusion_sdk/calvin_files/fusion/src
> -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter
> -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter
> -Ifusion_sdk/calvin_files/parameter/src
> -Ifusion_sdk/calvin_files/parsers/src
> -Ifusion_sdk/calvin_files/portability/src
> -Ifusion_sdk/calvin_files/template/src
> -Ifusion_sdk/calvin_files/utils/src
> -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file
> -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util
> -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2
> -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp -o
> fusion_sdk/calvin_files/data/src/CDFProbeInformation.o
> In file included from fusion_sdk/calvin_files/data/src/DataSet.h:25,
> from fusion_sdk/calvin_files/data/src/
> CDFProbeInformation.h:27,
> from
> fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp:21:
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:107: error:
> 'wstring' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:107: error:
> 'wstring' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:107: error:
> template argument 1 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:107: error:
> template argument 2 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:107: error:
> invalid type in declaration before ';' token
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:108: error:
> 'wstring' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:108: error:
> 'wstring' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:108: error:
> template argument 1 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:108: error:
> template argument 2 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:108: error:
> expected initializer before 'WStringVectorIt'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:109: error:
> 'wstring' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:109: error:
> 'wstring' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:109: error:
> template argument 1 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:109: error:
> template argument 2 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:109: error:
> expected initializer before 'WStringVectorConstIt'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:111: error:
> 'wstring' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:111: error:
> 'wstring' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:111: error:
> template argument 1 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:111: error:
> template argument 2 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:111: error:
> invalid type in declaration before ';' token
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:112: error:
> 'wstring' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:112: error:
> 'wstring' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:112: error:
> template argument 1 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:112: error:
> template argument 2 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:112: error:
> expected initializer before 'WStringListIt'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:113: error:
> 'wstring' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:113: error:
> 'wstring' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:113: error:
> template argument 1 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:113: error:
> template argument 2 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:113: error:
> expected initializer before 'WStringListConstIt'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:116: error:
> 'string' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:116: error:
> 'string' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:116: error:
> template argument 1 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:116: error:
> template argument 2 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:116: error:
> invalid type in declaration before ';' token
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:117: error:
> 'string' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:117: error:
> 'string' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:117: error:
> template argument 1 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:117: error:
> template argument 2 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:117: error:
> expected initializer before 'StringVectorIt'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:118: error:
> 'string' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:118: error:
> 'string' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:118: error:
> template argument 1 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:118: error:
> template argument 2 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:118: error:
> expected initializer before 'StringVectorConstIt'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:120: error:
> 'string' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:120: error:
> 'string' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:120: error:
> template argument 1 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:120: error:
> template argument 2 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:120: error:
> invalid type in declaration before ';' token
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:121: error:
> 'string' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:121: error:
> 'string' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:121: error:
> template argument 1 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:121: error:
> template argument 2 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:121: error:
> expected initializer before 'StringListIt'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:122: error:
> 'string' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:122: error:
> 'string' is not a member of 'std'
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:122: error:
> template argument 1 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:122: error:
> template argument 2 is invalid
> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:122: error:
> expected initializer before 'StringListConstIt'
> In file included from fusion_sdk/calvin_files/data/src/
> CDFProbeInformation.h:27,
> from
> fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp:21:
> fusion_sdk/calvin_files/data/src/DataSet.h:306: error: 'void
> affymetrix_calvin_io::DataSet::AssignValue(int32_t, WStringVector&,
> char*&)' cannot be overloaded
> fusion_sdk/calvin_files/data/src/DataSet.h:304: error: with 'void
> affymetrix_calvin_io::DataSet::AssignValue(int32_t, StringVector&,
> char*&)'
> make: *** [fusion_sdk/calvin_files/data/src/CDFProbeInformation.o]
> Error 1
> ERROR: compilation failed for package 'affxparser'
> ** Removing '/home/mkimpel/R_HOME/site-library-2.8.0/affxparser'
>
> The downloaded packages are in
> /tmp/RtmpFcVvk1/downloaded_packages
> Warning message:
> In install.packages("affxparser", repos = repos, configure.args =
> c("CC=/usr/bin/gcc-4.2", :
> installation of package 'affxparser' had non-zero exit status
>> sessionInfo()
> R version 2.8.0 Under development (unstable) (2008-08-27 r46445)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE
> =
> en_US
> .UTF
> -8
> ;LC_NUMERIC
> =
> C
> ;LC_TIME
> =
> en_US
> .UTF
> -8
> ;LC_COLLATE
> =
> en_US
> .UTF
> -8
> ;LC_MONETARY
> =
> C
> ;LC_MESSAGES
> =
> en_US
> .UTF
> -8
> ;LC_PAPER
> =
> en_US
> .UTF
> -8
> ;LC_NAME
> =
> C
> ;LC_ADDRESS
> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines tools stats graphics grDevices utils
> datasets
> [8] methods base
>
> other attached packages:
> [1] affycoretools_1.13.3 annaffy_1.13.1 KEGG.db_2.2.3
> [4] gcrma_2.13.1 matchprobes_1.13.1 biomaRt_1.15.1
> [7] RCurl_0.9-4 GOstats_2.7.0 Category_2.7.4
> [10] genefilter_1.21.3 survival_2.34-1 RBGL_1.17.2
> [13] annotate_1.19.2 xtable_1.5-3 GO.db_2.2.3
> [16] AnnotationDbi_1.3.9 RSQLite_0.7-0 DBI_0.2-4
> [19] limma_2.15.11 affy_1.19.4 preprocessCore_1.3.4
> [22] affyio_1.9.1 Biobase_2.1.7 graph_1.19.5
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.11 GSEABase_1.3.4 XML_1.96-0
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