[BioC] gcrma error? - linked to makeProbePackage ?

James W. MacDonald jmacdon at med.umich.edu
Fri Jul 6 16:21:07 CEST 2007

Hi Ben,

Benoit Ballester wrote:
> Cei Abreu-Goodger wrote:
>> Is there some reason for you not wanting to update your BioC 
>> distribution? It might even solve the problem you had with the 
>> matchprobes package...
> As far as I understand the BioC distrib is linked to the R version 
> installed.
> In my case I am using R (2.3.1) in a shared server, so having bioc1.8

Even on a shared server you should have enough space in your home 
directory to compile a current version of R. This IMO is the preferred 
way to go so you don't have to rely on your sysadmin to update things 
regularly (which obviously isn't happening for you).



>  > source("http://bioconductor.org/biocLite.R")
>  > biocLite(c("matchprobes"))
> Running biocinstall version 1.8.5 with R version 2.3.1
> Your version of R requires version 1.8 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = 
> dependencies,  :
>           argument 'lib' is missing: using 
> /ebi/research/biomart/benoit/R/R_LIB
> trying URL 
> 'http://bioconductor.org/packages/1.8/bioc/src/contrib/matchprobes_1.4.0.tar.gz'
> Content type 'application/x-gzip' length 7654424 bytes
> opened URL
> ==================================================
> downloaded 7475Kb
> * Installing *source* package 'matchprobes' ..
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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