[Bioc-devel] A bioconductor package archive?

Gabe Becker becker.gabe at gene.com
Wed Nov 18 18:50:59 CET 2015

Hi all,

Unless I'm missing something, there is no archive of prior source packages
for Bioconductor, in the vein of CRAN's Web Archive.  It has generally been
accepted, I think, that if you need a version of a package - e.g., for
precise reproducibility - you can go to the still-existing release
repository for that Bioc release, or to the svn.

The difficulty arises in determining where in the svn to look when the
old-release repo has a later version of the package. In my switchr package
I take the first commit with the requested version. This is generally
correct, but it isn't always (for example, I recently found it does not
work with IRanges version 1.20.5). Without a rule to automate the search
process that will work generally, the svn repository while  in principle
guaranteeing that a particular previous package can be re-created, does not
provide this in practice.

I know that going backwards and backfilling an archive of previous
Bioconductor package versions is not feasible, but would it be possible to
start populating an archive now moving forward - with the expectation that
they would be preserved indefinitely - to prevent this in the future?
Automated tagging of package releases within the SVN would probably also


Gabriel Becker, Ph.D
Associate Scientist
Bioinformatics and Computational Biology
Genentech Research

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