[BioC] getBioC and local repositories

[Seth Falcon]

mark garey <garey at biostat.ucsf.edu> writes:

> greetings all.
>
> i have checked the GMANE archive where i found a related
> solution at http://www.isrec.isb-sib.ch/~sengstag/bioc_mirror.html.
> an excellent resource, but here is my problem.
>
> i need to set up and maintain a local Bioconductor repository on a
> system where no outbound http protocols are allowed and maintenance
> for such a repository is restricted to an interactive node within a  
> research
> cluster ( so no fetching of remote files ).
>
> my question is can getBioc.R ( the other scripts ) be modified to  
> point to a local path where
> a Bioc package repository has been installed? that is, can it deal  
> with a file:/ type URL?

I believe so.  The biocLite/getBioc scripts are wrappers around R's
install.packages function.  I have used install.packages on a local
repository using file:// style URLs.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/