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Re: Bioconductor: Use SVN/git by default?

From: Ludovic Courtès
Subject: Re: Bioconductor: Use SVN/git by default?
Date: Fri, 01 Jul 2016 14:44:38 +0200
User-agent: Gnus/5.13 (Gnus v5.13) Emacs/24.5 (gnu/linux)


Ricardo Wurmus <address@hidden> skribis:

> 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
> useful.

For the record:

> 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.

Yeah, using SVN is a solution that would work right now, so if that
seems workable for you without too much work, go for it.


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