[BioC] errors with attempted installation of package affxparser

[Mark Kimpel]

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

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