From mboxrd@z Thu Jan 1 00:00:00 1970 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) Subject: Re: Bioconductor: Use SVN/git by default? Date: Fri, 01 Jul 2016 14:44:38 +0200 Message-ID: <87h9c9le89.fsf@gnu.org> References: <87vb17u9uk.fsf@gnu.org> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:43472) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bIxoN-00045q-Op for guix-devel@gnu.org; Fri, 01 Jul 2016 08:44:48 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bIxoJ-0005Dj-II for guix-devel@gnu.org; Fri, 01 Jul 2016 08:44:46 -0400 In-Reply-To: (Ricardo Wurmus's message of "Wed, 29 Jun 2016 16:51:39 +0200") List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Ricardo Wurmus Cc: guix-devel Hello! Ricardo Wurmus skribis: > Ludovic Court=C3=A8s writes: > >> Hi! >> >> Ricardo Wurmus 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=E2=80=99t gi= ve 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 =E2=80=9Cif=E2=80=9D, 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=E2=80=99.