On 07/01/2010 12:13 PM, Andr?s Rogers wrote: > Dear Chunlong, as you pointed out downgrading gcc to version 4.2 made > compilation possible. > > Thank you so much, cheers. GeneR version 2.18.1, appearing in the next day or so via biocLite, should address this problem. Thanks for the report. Martin > > 2010/7/1 Chunlong Chen <chen at="" cgm.cnrs-gif.fr=""> > >> Dear Andr??s, >> >> 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, Andr??s 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 funci??n ???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 funci??n >>> ???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 funci??n >>> ???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 at 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'??quipe Claude THERMES >> CNRS - Centre de G??n??tique Mol??culaire >> Avenue de la Terrasse - B??t. 24 >> 91198 Gif-sur-Yvette Cedex >> France >> >> Mail: chen at cgm.gif-cnrs.fr >> >> > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793