[Bioc-devel] A bioconductor package archive?

Hervé Pagès hpages at fredhutch.org
Wed Nov 18 19:47:39 CET 2015

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.


> Best,
> ~G
> Gabriel Becker, Ph.D
> Associate Scientist
> Bioinformatics and Computational Biology
> Genentech Research
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

More information about the Bioc-devel mailing list