[Bioc-devel] RPMs for Bioconductor from Biopackages
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 source.
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