[Bioc-devel] Packages available in the build system

[Nicolas Delhomme]

On 31 Mar 2012, at 20:16, Michael Lawrence wrote:

> 
> 
> On Sat, Mar 31, 2012 at 11:03 AM, Nicolas Delhomme <delhomme at embl.de> wrote:
> Hi Michael,
> 
> That's indeed something I'm considering too. I'm trying to figure out what's the best in my case. Thanks for the input!
> 
> 
> Ok. Bioc does support the use of Omegahat packages, but some of them can be difficult to build and are not very well maintained. That would be my main concern with Rcompression, although my fears may be unfounded.
> 

That's partly what motivated my question.

> If you're not aware already, you might check out the FaFile support in Rsamtools (razip'd files are efficient to query for particular sub-regions). Would only help if you're in control of the data source, of course.

Thanks, I wasn't. I'll have a look.

Cheers,

N.

>  
> 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
> ---------------------------------------------------------------
> 
> 
> 
> 
> 
> On 31 Mar 2012, at 19:46, Michael Lawrence 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. 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.
> >
> >
> > I think you can just use gzcon() for decompressing data, as long as you can get it into a connection, like via rawConnection(). gzcon supports gz, bz2 and xz, which sounds like more than Rcompression.
> >
> > Also, I'm wondering if RCurl is really necessary? Might gzcon(url(x)) fit your use case?
> >
> >
> >
> > 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
> >
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> 
>