[BioC] Error while installing genefilter package

Robert Gentleman rgentlem at fhcrc.org
Mon Oct 10 21:58:23 CEST 2005


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 
  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.


> 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]]
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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
rgentlem at fhcrc.org

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