From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: bioinformatics.scm vs bioconductor.scm ? Date: Wed, 12 Dec 2018 13:45:21 +0100 Message-ID: <87y38u52xq.fsf@elephly.net> References: <87a7lb5rza.fsf@elephly.net> 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]:58180) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gX3tR-0006tJ-P8 for guix-devel@gnu.org; Wed, 12 Dec 2018 07:45:38 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gX3tO-0005uF-Id for guix-devel@gnu.org; Wed, 12 Dec 2018 07:45:37 -0500 Received: from sender-of-o53.zoho.com ([135.84.80.218]:21806) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1gX3tO-0005sz-4J for guix-devel@gnu.org; Wed, 12 Dec 2018 07:45:34 -0500 In-reply-to: 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: zimoun Cc: Guix Devel zimoun writes: > Thank you the explanations. > > >> New Bioconductor packages should go to bioconductor.scm. Eventually we >> may move all remaining R packages from bioinformatics to >> bioconductor.scm. > > I am a bit confused. > The file bioconductor.scm contains (or will contain) all R packages > from Bioconductor, right? Correct. > But R packages from CRAN used in Bioinformatics ? bioconductor.scm or > bioinformatics.scm? Neither :) We put them in cran.scm. At least that=E2=80=99s the new way of doing this. Previously it was all ad-hoc, meaning that packages would end up in bioinformatics.scm=E2=80=A6 Ideally, bioinformatics.scm would only contain non-R tools like samtools, bamtools, bioinfo pipelines, etc. > And I am asking myself if a massive import from Bioconductor should be > possible ? Certainly! I=E2=80=99ve done this before actually, but I hit two minor problems: 1. the bioconductor recursive importer does not *automatically* switch to =E2=80=9CCRAN mode=E2=80=9D when a dependent package isn=E2=80=99t fo= und on Bioconductor. Not a big problem, but it means that teh import isn=E2=80=99t fully automatic. 2. compiling big Guile modules (such as a future (gnu packages cran)) require lots of memory since Guile 2.2(?), so I didn=E2=80=99t add all t= hese packages. This is a bug and we=E2=80=99d have to split the module, prob= ably, to work around it. -- Ricardo