[Bioc-devel] finding specific (outdated!)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

Dan Tenenbaum dtenenba at fhcrc.org
Tue Jul 9 06:53:45 CEST 2013

On Mon, Jul 8, 2013 at 9:14 PM, 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?

In the checked-out edgeR working directory, do:

svn log --diff DESCRIPTION > diff.txt

(this requires subversion >= 1.7)

Then look in diff.txt for "Version: 2.2.0". This ends up being revision 54800.

Then you can check that out to a different directory with
svn co -r54800 https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edgeR/


For more on the topic you bring up, see the thread started by

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