Re: Bioconductor: Use SVN/git by default?

[Ludovic Courtès]

Hello!

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:

  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’.