[Bioc-devel] RPMs for Bioconductor from Biopackages

Allen Day allenday at ucla.edu
Fri Jan 26 13:23:57 CET 2007

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


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

More information about the Bioc-devel mailing list