[BioC] GeneR fail to compile

[Robert Gentleman]

Hi,
   One issue might be that your gcc is too new. A number of packages 
needed to be repaired to deal with gcc 4.3.1. If your gcc is new, you 
could try to port the modification Herve made to GeneR in the devel 
branch (or you could see if the devel version 2.11.1 installs in your R)

  best wishes
    Robert


Pierre-Yves wrote:
> Dear list,
> 
> I am trying to install GeneR but it is facing a problem at compilation 
> time:
> 
> + R CMD INSTALL GeneR -l 
> /var/tmp/R-GeneR-2.10.0-1.fc9-root-builder/usr/lib64/R/library
> * Installing *source* package 'GeneR' ...
> ** libs
> g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe 
> -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic -c GeneR_glob.cc -o 
> GeneR_glob.o
> In file included from GeneR_glob.cc:14:
> GeneR_seq.h: In member function 'void GeneR_seq::setAccN(char*)':
> GeneR_seq.h:152: error: 'strlen' was not declared in this scope
> GeneR_seq.h:157: error: 'strncpy' was not declared in this scope
> GeneR_glob.cc: In member function 'void GeneR_glob::getAccno(int, char*, 
> int*)':
> GeneR_glob.cc:351: error: 'strncpy' was not declared in this scope
> make: *** [GeneR_glob.o] Error 1
> ERROR: compilation failed for package 'GeneR'
> ** Removing 
> '/var/tmp/R-GeneR-2.10.0-1.fc9-root-builder/usr/lib64/R/library/GeneR'
> error: Bad exit status from /var/tmp/rpm-tmp.20062 (%install)
> 
> 
> Has this error been already met ? Did I miss something ?
> 
> Thanks in advance for your help,
> 
> Regards,
> 
> Pierre
> 
> In case:
>  > sessionInfo()
> R version 2.7.2 (2008-08-25)
> x86_64-redhat-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US.utf8;LC_MONETARY=C;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICATION=C 
> 
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
> 
> other attached packages:
> [1] hgu95av2.db_2.0.2   AnnotationDbi_1.1.6 RSQLite_0.6-9
> [4] DBI_0.2-4           annaffy_1.11.0      KEGG_2.0.1
> [7] GO_2.0.1            Biobase_2.0.1
> 
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> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org