[BioC] GeneR fail to compile

Pierre-Yves pingou at pingoured.fr
Fri Oct 3 16:46:06 CEST 2008


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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