[BioC] Repository for Bioconductor annotation packages

James W. MacDonald jmacdon at med.umich.edu
Sat Jul 15 13:53:55 CEST 2006

Daniel Gatti wrote:
> 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",
>  >> repos="http://www.bioconductor.org")
>  >It's easier to use biocLite() instead.
>  >
>  >source("http://www.bioconductor.org/biocLite.R")
>  >biocLite("hgu133a")
> biocLite installs in the R library directory on the server.  

That's not true. biocLite() is simply a wrapper to install.packages() 
that among other things sets the correct repositories to iterate 
through. All you have to do is pass a lib argument and it will install 
wherever you want, just like install.packages().

 > biocLite("affy", lib="C:/Documents and Settings/dd1/Desktop/test")
Running getBioC version 0.1.6 with R version 2.3.0
Running biocinstall version 1.8.4 with R version 2.3.0
Your version of R requires version 1.8 of Bioconductor.
trying URL 
Content type 'application/zip' length 2230953 bytes
opened URL
downloaded 2178Kb

package 'affy' successfully unpacked and MD5 sums checked

The downloaded packages are in
         C:\Documents and Settings\dd1\Local 
updating HTML package descriptions
 > dir("C:/Documents and Settings/dd1/Desktop/test")
[1] "affy"

James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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