[Bioc-devel] RPMs for Bioconductor from Biopackages
Yeah, saw that. We have a stable and testing repository to handle that scenario. Bioconductor 2.0 will go into testing until it is released. We could conceivably put 1.9 in stable now, but we're shorthanded and don't have time to build it. Hence the call for participants. Thanks.
On 1/26/07, Martin Maechler <maechler at stat.math.ethz.ch> wrote:
"Allen" == Allen Day <allenday at ucla.edu>
on Thu, 25 Jan 2007 18:24:11 -0800 writes:
Allen> Hi,
Allen> This is a cross post to both the Biopackages discussion list and the
Allen> Bioconductor devel list.
Allen> I'm an RPM developer for the Biopackages project (
Allen> http://biopackages.net ). We've previously built Bioconductor 1.8 for
Allen> several different flavors and architectures of Fedora and CentOS.
Allen> This is handled by a SGE based build farm that we've developed for the
Allen> Biopackages project, article forthcoming.
Allen> Now we want to package the Bioconductor 2.0 devel packages.
and you know that this implies its users use R-devel aka
"R version x.y.z Under development (unstable) ......
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Of course that's nice for bioconductor *developers* who are
themselves willing to work with a bleeding-edge version of R
which can well be broken at times.
But packaging these things, means putting it into hands of useRs
who may be pretty clueless about the "unstable" part of the
underlying R version.
Hence, (as an R-core developer) I'm a bit nervous about the
dangers of such a deployment..
Regards,
Martin Maechler, ETH Zurich
Allen> It's a ton of work, there are ~200 of them. I'm hoping this mail will
Allen> stimulate collaboration between the two projects. Perhaps we can use
Allen> some of the code that does the daily Bioconductor testing in our build
Allen> farm, especially if it includes code for building dependency graphs
Allen> from the R modules, that is really the rate limiting step to building
Allen> the RPMs because we're currently encoding dependencies manually.
Allen> Hit me on either list or at allenday at ucla.edu if you'd like to
Allen> participate in building RPMs for Bioconductor. Thanks.
Allen> -Allen