[Bioc-devel] RPMs for Bioconductor from Biopackages

Seth Falcon sfalcon at fhcrc.org
Fri Jan 26 05:44:04 CET 2007

Hi Allen,

"Allen Day" <allenday at ucla.edu> writes:
> 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.

We'd be happy to share the code we use for our daily builds, although
I would be surprised if it is what you want.

If you want to build dependency graphs (and determine usable
installation order), there is code to do this in the pkgDepTools
package.  There is a vignette here:


and also an article in the R News newsletter linked from the R
homepage.  If you give this a try and have questions or other
feedback, please let me know.

+ seth

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