GeneR fail to compile
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Pierre-Yves ▴ 120
@pierre-yves-2963
Last seen 6.9 years ago
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.u tf8;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_IDENTIFICATI ON=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
hgu95av2 GeneR hgu95av2 GeneR • 654 views
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 6.2 years ago
United States
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_IDENTIFICA TION=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 > > _______________________________________________ > 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 > -- 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
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Robert Gentleman wrote: > 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) The version 2.11.1 compiles fine on my gcc 4.3.0 $ gcc --version gcc (GCC) 4.3.0 20080428 (Red Hat 4.3.0-8) Thanks for the help, Best regards, Pierre
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