Hi Gabe,
On 11/18/2015 09:50 AM, Gabe Becker wrote:
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
work.
I definitely want to add this tagging. I'm planning to do some work in
December to support incremental builds so we'll be able to switch
between "full build/check of everything" mode and "build/check modified
packages + packages that depend on them only" mode. I'll need to have
the SVN tag in the DESCRIPTION file for this. Will add it soon.
I'll let others speak for the bioconductor package archive.
Cheers,
H.
Best,
~G
Gabriel Becker, Ph.D
Associate Scientist
Bioinformatics and Computational Biology
Genentech Research
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Program in Computational Biology
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