[BioC] errors with attempted installation of package affxparser
Kasper Daniel Hansen
khansen at stat.berkeley.edu
Thu Aug 28 18:09:26 CEST 2008
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)
>
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