[Bioc-devel] RPMs for Bioconductor from Biopackages

Allen Day allenday at ucla.edu
Fri Jan 26 13:28:44 CET 2007


Thanks, pkgDepTools looks like what we need.  Some of that plotting
code may even end up being used for visualizing non-R RPM graphs.  Is
this package able to identify packages that are distributed with R and
not list them as dependencies?


On 1/25/07, Seth Falcon <sfalcon at fhcrc.org> wrote:
> 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:
>     http://www.bioconductor.org/packages/2.0/bioc/html/pkgDepTools.html
> 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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