[BioC] Affymetrix cdf-package question

[Laurent Gautier]

Jeff Gentry wrote:
>>please let me know.) My question is this. When Bioconductor tries to 
>>install CDF package, it tries to do it globally, I mean it requires 
>>some root-level security privilege to install the necessary CDF 
>>package. Is there any way that this can be done locally, that is make 
>>Bioconductor install the necessary CDF package in a user's local 
>>directory and fetch gene-information from it, which will not require 
>>root-level privilege?
> 
> 
> I'm not 100% sure of exactly how they handle things in affy to call the
> reposTools functions but I believe that the way you want
> to go about this is to put the directory that you wish to use
> .libPaths() to specify the directory you want the pacakges installed into.
> 
> If you call '.libPaths(<dir>)', that will place the new directory in the
> front of your library path setting, and I believe that affy is taking the
> first one in that vector.


Yes, by default .libPaths[1] is used.

Changing the destination directory for Cdf  is explained in the 
following vignette:
http://www.bioconductor.org/repository/devel/vignette/dealing_with_cdfenvs.pdf



L.




> -J
> 
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