[BioC] Repository for Bioconductor annotation packages

Keith Satterley keith at wehi.EDU.AU
Mon Jul 17 01:38:59 CEST 2006


Further to where one can find the annotation data. I notice that when I 
install R2.3.1 on my Windows computer, the Select Repositories option 
shows 4 sites, CRAN, CRAN(extras), Bioconductor and Omegahat. If I add 
the following line:

BioCMData	BiocMetaData 
http://www.bioconductor.org/packages/data/annotation	FALSE	TRUE	TRUE	FALSE

(This is one long line)
to the repositories file in my R-2.3.1\etc subdirectory, I then have an 
extra repository listed, called BiocMetaData and I can then (provided I 
select it as a repository) see all the annotation data packages listed 
when I use Install Packages from the Packages Menu of the RGui.
Can this repository option be added automatically to the Repositories 
file when R is installed

Keith Satterley

James W. MacDonald wrote:
> Hi Daniel,
> Daniel Gatti wrote:
>>O/S: Linux
>>arch : i686
>>R version : 2.2.1
>>I'm using the install.packages() command to install Bioconductor 
>>libraries to my home directory.  I can install functional packages like 
>>"safe" and "GOstats". But when I try to install annotation packages, it 
>>tells me that it can't find them in given repository.  I'm using 
>>repos="http://www.bioconductor.org".  What repository should I use for 
>>the annotation packages?
>>install.packages("hgu133a", lib = "~/Rlib", 
> It's easier to use biocLite() instead.
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("hgu133a")
> HTH,
> Jim
>>Warning in download.packages(pkgs, destdir = tmpd, available = 
>>available,  :
>>          no package 'hgu133a' at the repositories
>>Dan Gatti
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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