From: ludo@gnu.org (Ludovic Courtès)
To: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Cc: guix-devel <guix-devel@gnu.org>
Subject: Re: Bioconductor: Use SVN/git by default?
Date: Fri, 01 Jul 2016 14:44:38 +0200 [thread overview]
Message-ID: <87h9c9le89.fsf@gnu.org> (raw)
In-Reply-To: <idj37nwvyis.fsf@bimsb-sys02.mdc-berlin.net> (Ricardo Wurmus's message of "Wed, 29 Jun 2016 16:51:39 +0200")
Hello!
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> Ludovic Courtès <ludo@gnu.org> writes:
>
>> Hi!
>>
>> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> 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:
https://sympa.inria.fr/sympa/arc/swh-devel/2016-06/msg00007.html
> 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.
Thanks,
Ludo’.
next prev parent reply other threads:[~2016-07-01 12:44 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-06-17 8:54 Bioconductor: Use SVN/git by default? Ricardo Wurmus
2016-06-17 15:13 ` Ludovic Courtès
2016-06-29 14:51 ` Ricardo Wurmus
2016-07-01 12:44 ` Ludovic Courtès [this message]
2016-06-30 2:44 ` Ben Woodcroft
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