[BioC] errors with attempted installation of package affxparser

[Kasper Daniel Hansen]

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
>
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> (317) 663-0513 Home (no voice mail please)
>
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