[Bioc-devel] Packages available in the build system

Hervé Pagès hpages at fhcrc.org
Mon Apr 2 07:33:53 CEST 2012

Hi Nico, Dan,

On 03/31/2012 12:00 PM, Dan Tenenbaum wrote:
> On Sat, Mar 31, 2012 at 9:46 AM, Nicolas Delhomme<delhomme at embl.de>  wrote:
>> Hi,
>> I'm thinking about using the Rcompression library for a package I'm writing and it is only available from the http://www.omegahat.org/R repository. I was wondering if this repo was used by the Bioc build system.
> No, it is not.
> You can see the repositories used by the build system if you do this:
> library(BiocInstaller)
> biocinstallRepos()

I should add to this that we can exceptionally drop in our extra repo
a package not available in the repos listed by biocinstallRepos() but
needed by a BioC software package. Currently most of the stuff in our
extra repo is actually stuff from Omegahat:


I said exceptionally because the maintenance of the extra repo is
kind of a burden (no build system of course so packages need to be
updated manually and the binaries made "by hand"). So the less packages
there the better.


> Dan
>> If not, I'd welcome pointers to libraries with similar capabilities, e.g. I'm retrieving compressed fasta files with Rcurl and would like to uncompress them in R.
>> Thanks!
>> Nico
>> ---------------------------------------------------------------
>> Nicolas Delhomme
>> Genome Biology Computational Support
>> European Molecular Biology Laboratory
>> Tel: +49 6221 387 8310
>> Email: nicolas.delhomme at embl.de
>> Meyerhofstrasse 1 - Postfach 10.2209
>> 69102 Heidelberg, Germany
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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