From: Ricardo Wurmus <rekado@elephly.net>
To: zimoun <zimon.toutoune@gmail.com>
Cc: Guix Devel <guix-devel@gnu.org>
Subject: Re: bioinformatics.scm vs bioconductor.scm ?
Date: Wed, 12 Dec 2018 13:45:21 +0100 [thread overview]
Message-ID: <87y38u52xq.fsf@elephly.net> (raw)
In-Reply-To: <CAJ3okZ1myBdQNyF1utkP66Ayoky1K8EL=utJsPxqu_vAeQ4+Ow@mail.gmail.com>
zimoun <zimon.toutoune@gmail.com> 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’s the new way of
doing this. Previously it was all ad-hoc, meaning that packages would
end up in bioinformatics.scm…
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’ve done this before actually, but I hit two minor
problems:
1. the bioconductor recursive importer does not *automatically* switch
to “CRAN mode” when a dependent package isn’t found on Bioconductor.
Not a big problem, but it means that teh import isn’t 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’t add all these
packages. This is a bug and we’d have to split the module, probably,
to work around it.
--
Ricardo
next prev parent reply other threads:[~2018-12-12 12:45 UTC|newest]
Thread overview: 10+ messages / expand[flat|nested] mbox.gz Atom feed top
2018-12-11 18:21 bioinformatics.scm vs bioconductor.scm ? zimoun
2018-12-12 3:44 ` Ricardo Wurmus
2018-12-12 11:42 ` zimoun
2018-12-12 12:45 ` Ricardo Wurmus [this message]
2018-12-18 11:31 ` zimoun
2018-12-18 18:26 ` Björn Höfling
2018-12-18 18:36 ` zimoun
2018-12-18 22:49 ` Ricardo Wurmus
2018-12-18 22:45 ` Ricardo Wurmus
2018-12-20 8:46 ` Ricardo Wurmus
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