Dear Chunlong, as you pointed out downgrading gcc to version 4.2 made
compilation possible.

Thank you so much, cheers.

2010/7/1 Chunlong Chen <chen@cgm.cnrs-gif.fr>

> Dear Andrés,
>
> Perhaps you can try to use the gcc 4.2 instead. I also got compiling
> problem of GeneR when using gcc >4.2.
>
> Best wishes,
>
> Chunlong
>
> On Wed, 2010-06-30 at 18:11 -0400, Andrés Rogers wrote:
> > Hello bioconductor community, this is my first post so please excuse me
> if i
> > make any protocol mistake, also please note that english is not my native
> > language.
> >
> > I'm trying to install the package GeneR (
> > http://bioconductor.org/packages/release/bioc/html/GeneR.html)
> > but for some reason i can't complete the compilation process.
> >
> > Im currently using Archlinux, R 2.11 , gcc 4.5 and the stable release of
> > Bioconductor (2.6).
> >
> > Here is what i'm doing (i have already installed other packages without
> > problem)
> >
> > sudo R
> > > source("http://bioconductor.org/biocLite.R")
> > > biocLite("GeneR")
> >
> > and here is the output:
> >
> > ...
> > * installing *source* package ‘GeneR’ ...
> > ** libs
> > g++ -I/usr/include/R/  -I/usr/local/include    -fpic  -march=i686
> > -mtune=generic -O2 -pipe -c GeneR_glob.cc -o GeneR_glob.o
> > g++ -I/usr/include/R/  -I/usr/local/include    -fpic  -march=i686
> > -mtune=generic -O2 -pipe -c GeneR_seq.cc -o GeneR_seq.o
> > g++ -I/usr/include/R/  -I/usr/local/include    -fpic  -march=i686
> > -mtune=generic -O2 -pipe -c complementaire.cc -o complementaire.o
> > g++ -I/usr/include/R/  -I/usr/local/include    -fpic  -march=i686
> > -mtune=generic -O2 -pipe -c compoSeq.cc -o compoSeq.o
> > compoSeq.cc: En la función ‘void sys_exactmatch(int*, char**, int*, int*,
> > int*, int*, int*, int*, int*, int*, int*, int*)’:
> > compoSeq.cc:77:9: error: no hay coincidencias al convertir la función
> > ‘strstr’ al tipo ‘char* (*)(const char*, const char*)’
> > /usr/include/string.h:329:1: error: los candidatos son: char*
> strstr(char*,
> > const char*)
> > /usr/include/string.h:335:1: error:                     const char*
> > strstr(const char*, const char*)
> > compoSeq.cc:81:11: error: no hay coincidencias al convertir la función
> > ‘strcasestr’ al tipo ‘char* (*)(const char*, const char*)’
> > /usr/include/string.h:367:20: error: los candidatos son: char*
> > strcasestr(char*, const char*)
> > /usr/include/string.h:369:28: error:                     const char*
> > strcasestr(const char*, const char*)
> > make: *** [compoSeq.o] Error 1
> > ERROR: compilation failed for package ‘GeneR’
> > * removing ‘/usr/lib/R/library/GeneR’
> > ...
> >
> > any help is much appreciated, as i'm needing this for my master thesis
> work,
> > thanks!
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> --
> Chunlong CHEN
> Post-doc
> L'équipe Claude THERMES
> CNRS - Centre de Génétique Moléculaire
> Avenue de la Terrasse - Bât. 24
> 91198 Gif-sur-Yvette Cedex
> France
>
> Mail: chen@cgm.gif-cnrs.fr
>
>


-- 
Andres Rogers
Licenciado en Cs. de la Ingeniería, U. de Chile
Estudiante de Ing. Civil mención Biotecnología y Magister en Ing. Química,
U. de Chile

	[[alternative HTML version deleted]]

