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Re: bioinformatics.scm vs bioconductor.scm ?
From: |
Ricardo Wurmus |
Subject: |
Re: bioinformatics.scm vs bioconductor.scm ? |
Date: |
Wed, 12 Dec 2018 13:45:21 +0100 |
User-agent: |
mu4e 1.0; emacs 26.1 |
zimoun <address@hidden> 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