[Bioc-devel] building R and bioconductor

Gabe Becker becker.gabe at gene.com
Tue Apr 28 19:58:03 CEST 2015


On Tue, Apr 28, 2015 at 10:52 AM, Martin Morgan <mtmorgan at fredhutch.org>

> Downloading a specific version of Bioconductor packages retrospectively is
> challenging, unless the version is the final version in a release cycle.
> This is because the Bioc repository only contains one version of a package
> for each release, and while it is might be possible to dissect the svn logs
> of individual packages to identify when a DESCRIPTION file had a particular
> version, there may be several svn commits associated with the version
> (packages are only pushed to the public repository when a version changes
> at the time the build starts each day, so the first svn revision would be a
> good [but not infallible] bet as to the revision that was made public).

This is true. switchr does this via the heuristic that you suggest. The
model here is that a version bump (in SVN/github/etc) represents a new
version of the package, and that all changes between version bumps simply
accumulate but do not "arrive" until the next version of the pacakge.

> If you wish to take a snapshot 'now' and have it available in the future,
> then the tools Laurent mentions might be appropriate. I think I would
> rather (but maybe I'm just perverse in this respect) rsync (
> http://bioconductor.org/about/mirrors/mirror-how-to/ and similar for
> CRAN) or manually create a 'CRAN-style' repository of source packages, and
> simply use this as the 'repos' argument (including pointing to a local file
> system) in install.packages.

Again, switchr does this via a concept called "lazy repositories", which
are built on demand with only the required packages, but that is how
dependencies between packages are supported, even when those packages don't
currently reside in any repository.


Gabriel Becker, Ph.D
Computational Biologist
Genentech Research

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