[BioC] errors with attempted installation of package affxparser
Kasper Daniel Hansen
khansen at stat.berkeley.edu
Thu Aug 28 20:31:47 CEST 2008
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
>>
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