[BioC] errors with attempted installation of package affxparser
Mark Kimpel
mwkimpel at gmail.com
Thu Aug 28 18:21:01 CEST 2008
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
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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