[Bioc-devel] RPMs for Bioconductor from Biopackages

M. Edward (Ed) Borasky znmeb at cesmail.net
Fri Jan 26 04:00:31 CET 2007

Allen Day wrote:
> Hi,
> This is a cross post to both the Biopackages discussion list and the
> Bioconductor devel list.
> I'm an RPM developer for the Biopackages project (
> http://biopackages.net ).  We've previously built Bioconductor 1.8 for
> several different flavors and architectures of Fedora and CentOS.
> This is handled by a SGE based build farm that we've developed for the
> Biopackages project, article forthcoming.
> Now we want to package the Bioconductor 2.0 devel packages.  It's a
> ton of work, there are ~200 of them.  I'm hoping this mail will
> stimulate collaboration between the two projects.  Perhaps we can use
> some of the code that does the daily Bioconductor testing in our build
> farm, especially if it includes code for building dependency graphs
> from the R modules, that is really the rate limiting step to building
> the RPMs because we're currently encoding dependencies manually.
> Hit me on either list or at allenday at ucla.edu if you'd like to
> participate in building RPMs for Bioconductor.  Thanks.
> -Allen
I'd be interested in the general structure and tools for integrating R 
package dependencies with Linux dependencies, and I suspect Dirk 
Eddelbuettel, who maintains the *Debian* packages for a large number of 
R packages, might be as well. I don't currently use or even have access 
to an RPM-based (or Debian-based) Linux system, however -- everything I 
do is on Gentoo. I'd certainly be willing to help out with any generic R 
/ Gentoo packaging integration projects. Gentoo "packages", which are 
called "ebuilds", are simply shell scripts that install a package from 
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M. Edward (Ed) Borasky, FBG, AB, PTA, PGS, MS, MNLP, NST, ACMC(P)

If God had meant for carrots to be eaten cooked, He would have given rabbits fire.

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