[Bioc-devel] Packages available in the build system

[Hervé Pagès]

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:

   http://bioconductor.org/packages/2.10/extra/

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.

Cheers,
H.

>
> 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

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