[Bioc-devel] RPMs for Bioconductor from Biopackages

Seth Falcon sfalcon at fhcrc.org
Fri Jan 26 16:14:49 CET 2007

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

> Seth,
> Thanks, pkgDepTools looks like what we need.  Some of that plotting
> code may even end up being used for visualizing non-R RPM graphs.

Should work once you add code to read non-R package description files
to create a DAG.  If you add such code, I will add it to the package.

> Is this package able to identify packages that are distributed with
> R and not list them as dependencies?

Yes.  Here's what the man page for makeDepGraph says about its
keep.builtin argument:

  keep.builtin: logical value indicating whether or not packages that
            come with a default R installation should be included in the
            nodes of the dependency graph.  The default, 'FALSE', is to
            remove these packages from the return result.

A few other notes on using pkgDepTools:

  * You will get much better performance if you set dosize=FALSE.
    When TRUE, the code uses RCurl to fetch the HTTP header of each
    package it encounters to estimate download size.  This is slow.

  * When calling getInstallOrder, you will probably want to set
    needed.only=FALSE so that you get a complete list and ignore
    whatever packages you happen to have installed at the time.

+ seth

PS: I think it is smart to target BioC 2.0 since it is going to take
some time to refine your process.  If you started with 1.9, then by
the time you had everything in place, it would be time to switch to

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