[BioC] Error installing genefilter

[Wolfgang Huber]

Hola Marcelo,

three points:

1. It looks like you don't have a Fortran compiler (g77) installed, or 
it's not in your Unix path. How did you install R?

2. For various reasons, I would consider it safer to run R CMD INSTALL 
*not as root*, but just as a normal user with restricted rights and just 
write permissions to the library directory.

3. You might want to get the newest (development) version of genefilter 
(1.6.1) - if you want to use rowFtests. If you need to work with 
bioconductor release 1.5, the rowFtests function is in the package 
"arrayMagic" there.

  Best regards
   Wolfgang


Marcelo Luiz de Laia wrote:
> Hi,
> 
> When I try to install package genefilter, I receive this error message:
> 
> root at lbmsala4b:/home/kurumin/Temp# R CMD INSTALL -l /usr/lib/R/library 
> genefilter_1.5.0.tar.gz
> * Installing *source* package 'genefilter' ...
> ** libs
> gcc -I/usr/lib/R/include     -fPIC  -g -O2 -c genedist.c -o genedist.o
> gcc -I/usr/lib/R/include     -fPIC  -g -O2 -c init.c -o init.o
> g77   -fPIC  -g -O2 -c ttest.f -o ttest.o
> make: g77: Comando não encontrado
> make: ** [ttest.o] Erro 127
> ERROR: compilation failed for package 'genefilter'
> ** Removing '/usr/lib/R/library/genefilter'
> ** Restoring previous '/usr/lib/R/library/genefilter'
> root at lbmsala4b:/home/kurumin/Temp#
> 
>  >sessionInfo
> 
> R version 2.0.1, 2004-11-15, i386-pc-linux-gnu
> 
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" 
> "utils"   [7] "datasets"  "base"   
> other attached packages:
> geneplotter    annotate         vsn        affy  reposTools     Biobase
>    "1.5.2"     "1.5.1"     "1.5.0"     "1.5.8"     "1.5.2"     "1.5.0"
>      limma
>    "1.9.0"
> 
> My gcc is more new.
> 
> How I solve this problem?
> 
> Thanks
> 
> Marcelo
> 
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> 


-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber