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Re: Bioconductor: Use SVN/git by default?

From: Ricardo Wurmus
Subject: Re: Bioconductor: Use SVN/git by default?
Date: Wed, 29 Jun 2016 16:51:39 +0200
User-agent: mu4e 0.9.16; emacs 24.5.1

Ludovic Courtès <address@hidden> writes:

> Hi!
> Ricardo Wurmus <address@hidden> skribis:
>> The lack of an archive is also a problem for reproducibility.  You
>> simply cannot download an archive for an obsolete package version.
> [...]
>> What do you think?  I see no way around using the sources from the
>> central Bioconductor SVN repository as tarballs simply don’t give us
>> what we need in terms of reproducibility.
> Would it help if we had access to a universal content-addressed archive
> that would include everything Bioconductor has ever published?
> That could be another solution (with a big “if”, granted ;-)).

I guess this would work too, but it would have to be comprehensive to be

The advantage of using SVN is that a user could quite easily create
variants of a set of Bioconductor R packages for a particular version of
the Bioconductor SVN repository.  This gives them additional granularity
which makes the fluidity of the Bioconductor releases more manageable.

Another advantage is that SVN exists right now.  It already behaves like
a full-blown archive of all Bioconductor packages, even *between*
Bioconductor releases.  It is just a little more cumbersome to access.

In any case, I think this would be an improvement over what we have
now.  Right now Bioconductor packages in Guix simply are not
reproducible over time.  As this invalidates the method of fully
describing a software environment symbolically (using a git hash of the
Guix repository and a manifest), I think we should build Bioconductor
packages from SVN to fix this.

~~ Ricardo

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