From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: Bioconductor: Use SVN/git by default? Date: Wed, 29 Jun 2016 16:51:39 +0200 Message-ID: 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]:44237) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bIGqJ-0004GL-82 for guix-devel@gnu.org; Wed, 29 Jun 2016 10:51:56 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bIGqE-0005Oa-8g for guix-devel@gnu.org; Wed, 29 Jun 2016 10:51:54 -0400 In-Reply-To: <87vb17u9uk.fsf@gnu.org> 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: Ludovic =?utf-8?Q?Court=C3=A8s?= Cc: guix-devel 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 g= ive 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, grante= d ;-)). I guess this would work too, but it would have to be comprehensive to be useful. 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