[Bioc-devel] finding specific (outdated!) bioc package archives?

Martin Morgan mtmorgan at fhcrc.org
Tue Jul 9 06:47:45 CEST 2013

It's actually ambiguous. The best that can be done is to bisect the svn log for the commit that is consistent with the date stamp in packageDescription("edgeR"). This would be from the command line and in the branch for the appropriate release

svn log -v https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/edgeR|less

It seems reasonable and feasible for the Bioc build process to add the svn revision to the package description. Obviously this would only help for packages currently being built.

----- Ross Lazarus <ross.lazarus at channing.harvard.edu> wrote:
> Hi, Bioconductor devs,
> In very rare cases (eg
> http://article.gmane.org/gmane.science.biology.informatics.conductor/35266/match=update+edgeR)
> where BioC package authors have released an urgent bug fix within a given
> BioC update cycle, the usual automated biocLite installation process does
> not appear to support recreating a very specific R/Bioc environment
> containing a precisely specified package release (say the previous edgeR
> 2.2.0 fixed by 2.2.5). You might argue a user should never do this, but
> since we want truly reproducible analyses (the context is the new toolshed
> dependency control mechanisms in Galaxy), we need to control *all*
> dependencies for a given release of a (eg edgeR) wrapper at this very fine
> level of granularity, acknowledging that reproducible =/= valid.
> Take that edgeR update as a test case. I know about
> http://bioconductor.org/checkResults/ and eg
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edgeR/ but I
> have been unable to figure out how to track down the 2.2.0 edgeR archive
> (or for that matter the 2.2.5 bugfix) - I'm sure it is in svn somewhere.
> Any advice on how I can identify a long term reliable svn or other url to
> script the download of a specific (even if know buggy) historical archive
> of (eg) edgeR 2.2.0?
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