[Bioc-devel] building R and bioconductor
Martin, On Tue, Apr 28, 2015 at 10:52 AM, Martin Morgan <mtmorgan at fredhutch.org> wrote:
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. Best, ~G
Gabriel Becker, Ph.D Computational Biologist Genentech Research [[alternative HTML version deleted]]