[Bioc-devel] Meta-information about bioc and bioc-package releases

Gabe Becker becker.gabe at gene.com
Wed May 27 19:31:43 CEST 2015

Hey all,

I've been wondering if bioc could offer a way to query information about
itself similar - though not necessarily identical -  to what Gabor Csardi's
(cc'ed) crandb offers http://www.r-pkg.org/services#api

Basically, I would really like two things, in increasing order of

#1: A webservice to easily determine the Bioc release version associated
with a particular version of R.

R knows how to do this itself, but it doesn't share the wealth (function
not exported) so I can't get at that without a NOTE which blocks submission
to CRAN.

Note that I explicitly do not want to require or depend on the presence of
BiocInstaller. Depending on BiocInstaller would prevent switchr from
allowing context switching between Bioc versions, which is a major use-case
for the software.

Something as simple as a web service which accepts an R version string and
spits out the Bioc release number would be sufficient, though a way to get
the full repo URLs would be a nice bonus

#2: A crandb-like database of Bioc package version releases.

The queries that I would specifically like, in the context of
reproducibility with my switchr package, are:

   - Which exact package versions were available on a specific date
   - Start and end dates for a given release of bioc
   - What date was a specific package version first released, and the span
   dates it was available via (a) repo
   - Dependency and reverse dependency information for each release of each
   - Given a package version, the smallest set of packages necessary to
   install the package, and the versions of those dependencies that were
   concurrent with the initial release, midpoint, and last moment before being
   superceded for the package in question. (crandb does not offer this; I can
   do it with many seperate calls, but it seems like the computation should be
   server-side for this). Peferably with or without including Suggests.
   Depending on implementation this could be completely or partially
   pre-computed for efficiency.
   - A mapping from package versions in repositories to SVN branch and
   commit, if possible.
   - Possibly other stuff crandb tracks.

Would one or both of these be possible?

I looked at using the crandb code directly, but it pulls from
<cranmirror>/src/contrib/Meta/archive.rds to get all of this information,
and that file either doesn't exist or isn't readable in the Bioc
repositories.  If we were to change that, I think a lot of what crandb
offers would come nearly for free, the only work being adding things that
crandb doesn't offer (the tree-shaking and version to svn mapping, for


Gabriel Becker, Ph.D
Computational Biologist
Genentech Research

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list