errors with attempted installation of package affxparser
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Mark W Kimpel ▴ 830
@mark-w-kimpel-2027
Last seen 10.2 years ago
I'm getting a string of errors when attempting to install affxparser. I'm using Debian Lenny and have both gcc-4.2 and 4.3 available. I've tried using the latest R-devel and R-2.7.2. I know there have been some reported problems with installation using gcc-4.3. Below is output from my last attempt using R-2.7.0 and gcc-4.2: install.packages("affxparser", repos= biocReposList(), configure.args = c('CC=/usr/bin/gcc-4.2', 'CXX=/usr/bin/g++-4.2')) 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 ..... many more lines > sessionInfo() R version 2.7.1 Patched (2008-07-07 r46046) 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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] affycoretools_1.12.1 annaffy_1.12.1 KEGG.db_2.2.0 [4] gcrma_2.12.1 matchprobes_1.12.1 biomaRt_1.14.1 [7] RCurl_0.9-4 GOstats_2.6.0 Category_2.6.0 [10] genefilter_1.20.0 survival_2.34-1 RBGL_1.16.0 [13] annotate_1.18.0 xtable_1.5-3 GO.db_2.2.0 [16] AnnotationDbi_1.2.2 RSQLite_0.7-0 DBI_0.2-4 [19] limma_2.14.6 affy_1.18.2 preprocessCore_1.2.1 [22] affyio_1.8.1 Biobase_2.0.1 graph_1.18.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 XML_1.96-0 -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please)
GO affxparser GO affxparser • 1.6k views
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@kasper-daniel-hansen-2979
Last seen 17 months ago
United States
Hi Mark As you have noticed this problem is known when using GCC 4.3 and we are trying to come up with a fix. That the problem also persists with GCC 4.2 is new to me. Could you Cut'n'paste the entire compilation command so that we can see what options you pass to the compiler? If (by any chance) you are capable of giving us ssh access to your machine for a week or so, it will help us come up with a fix. It is hard to debug when we don't have access to GCC 4.3 ourselves. So apart from sending me the entire compilation command you probably cannot do much but wait. Kasper On Aug 28, 2008, at 7:43 AM, Mark Kimpel wrote: > I'm getting a string of errors when attempting to install affxparser. > I'm using Debian Lenny and have both gcc-4.2 and 4.3 available. I've > tried using the latest R-devel and R-2.7.2. I know there have been > some reported problems with installation using gcc-4.3. Below is > output from my last attempt using R-2.7.0 and gcc-4.2: > > install.packages("affxparser", repos= biocReposList(), configure.args > = c('CC=/usr/bin/gcc-4.2', 'CXX=/usr/bin/g++-4.2')) > > 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 ..... many more lines > >> sessionInfo() > R version 2.7.1 Patched (2008-07-07 r46046) > 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_1.12.1 annaffy_1.12.1 KEGG.db_2.2.0 > [4] gcrma_2.12.1 matchprobes_1.12.1 biomaRt_1.14.1 > [7] RCurl_0.9-4 GOstats_2.6.0 Category_2.6.0 > [10] genefilter_1.20.0 survival_2.34-1 RBGL_1.16.0 > [13] annotate_1.18.0 xtable_1.5-3 GO.db_2.2.0 > [16] AnnotationDbi_1.2.2 RSQLite_0.7-0 DBI_0.2-4 > [19] limma_2.14.6 affy_1.18.2 preprocessCore_1.2.1 > [22] affyio_1.8.1 Biobase_2.0.1 graph_1.18.1 > > loaded via a namespace (and not attached): > [1] cluster_1.11.11 XML_1.96-0 > > -- > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 663-0513 Home (no voice mail please) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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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/affx parser_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/FusionCHPQuantificationDetectionDat a.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/CHPQuantificationDetectionFileRead er.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 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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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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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/af fxparser_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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Hi, Kasper, since you're more familar with the Makefile of affxparser, would it be possible to output details on the version of the gcc compiler at the beginning of the build such that it is added to the log? Just an idea /Henrik On Thu, Aug 28, 2008 at 9:35 AM, Kasper Daniel Hansen <khansen at="" stat.berkeley.edu=""> wrote: > 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/CalvinCELDataAdapt er.o >> fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapt er.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/FusionCHPQuantificationDetection Data.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/CHPQuantificationDetectionFileR eader.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;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Entering edit mode
On Aug 28, 2008, at 11:04 AM, Henrik Bengtsson wrote: > Hi, > > Kasper, since you're more familar with the Makefile of affxparser, > would it be possible to output details on the version of the gcc > compiler at the beginning of the build such that it is added to the > log? > > Just an idea Well, I guess it could be possible. We might have to move to a Makefile instead of Makevars, which I am loathe to do. These days it is easy to get a handle on the compiler used since R now has R CMD config CC which reports the compiler. It would be a bit nicer to have it in the log, but I am not sure it would be worth the effort. Kasper > /Henrik > > > On Thu, Aug 28, 2008 at 9:35 AM, Kasper Daniel Hansen > <khansen at="" stat.berkeley.edu=""> wrote: >> 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >>
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