Error compiling GeneR package
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@andres-rogers-4149
Last seen 6.9 years ago
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]]
PROcess GeneR PROcess GeneR • 779 views
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@andres-rogers-4149
Last seen 6.9 years ago
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]]
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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
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