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Hi, Nayeem Quayum wrote: > Hello to everybody.. I am trying to install genefilter package from R using > the command > biocLite("genefilter") > but it gave me error > * Installing *source* package 'genefilter' ... > ** libs > gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -fomit- frame-pointer > -pipe -march=i586 -mtune=pentiumpro -c genedist.c -o genedist.o > gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -fomit- frame-pointer > -pipe -march=i586 -mtune=pentiumpro -c init.c -o init.o > gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -fomit- frame-pointer > -pipe -march=i586 -mtune=pentiumpro -c rowttests.c -o rowttests.o > f95 -fPIC -O2 -fomit-frame-pointer -pipe -march=i586 -mtune=pentiumpro -c > ttest.f -o ttest.o > make: f95: Command not found So, R is configured to believe that there is a f95 around and there is not. Reconfiguring R to use a Fortran compiler you have, fixing your path if f95 is installed but not on your path, or installing an appropriate f95 seem like your alternatives. (I really don't think you want f95 btw all of our fortran code should be f77 compatible) Note this has nothing to do with Bioconductor packages, but rather is a misconfiguration of your system. Robert > make: *** [ttest.o] Error 127 > ERROR: compilation failed for package 'genefilter' > ** Removing '/usr/lib/R/library/genefilter' > ** Restoring previous '/usr/lib/R/library/genefilter' > > The downloaded packages are in > /root/tmp/RtmpE11972/downloaded _packages > Warning message: > installation of package 'genefilter' had non-zero exit status in: > install.packages(pkgs = "genefilter", repos = c(" > http://www.bioconductor.org/packages/bioc/stable", > I am running R in Mandriva. Please any body help me out how to solve this > problem. Thanks. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- 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

Hi Nayeem, The line: make: f95: Command not found shows what the problem is. you're missing a fortran compiler in there, is it possible that this is not the same machine as you compiled R with in the first place? GCC can handle fortran compilation, but I'm not quite sure where you would have to change those settings. Maybe someone can offer some better help with this. Francois On Mon, 2005-10-10 at 13:39 -0600, Nayeem Quayum wrote: > Hello to everybody.. I am trying to install genefilter package from R using > the command > biocLite("genefilter") > but it gave me error > * Installing *source* package 'genefilter' ... > ** libs > gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -fomit- frame-pointer > -pipe -march=i586 -mtune=pentiumpro -c genedist.c -o genedist.o > gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -fomit- frame-pointer > -pipe -march=i586 -mtune=pentiumpro -c init.c -o init.o > gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -fomit- frame-pointer > -pipe -march=i586 -mtune=pentiumpro -c rowttests.c -o rowttests.o > f95 -fPIC -O2 -fomit-frame-pointer -pipe -march=i586 -mtune=pentiumpro -c > ttest.f -o ttest.o > make: f95: Command not found > make: *** [ttest.o] Error 127 > ERROR: compilation failed for package 'genefilter' > ** Removing '/usr/lib/R/library/genefilter' > ** Restoring previous '/usr/lib/R/library/genefilter' > > The downloaded packages are in > /root/tmp/RtmpE11972/downloaded _packages > Warning message: > installation of package 'genefilter' had non-zero exit status in: > install.packages(pkgs = "genefilter", repos = c(" > http://www.bioconductor.org/packages/bioc/stable", > I am running R in Mandriva. Please any body help me out how to solve this > problem. Thanks. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >