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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?


> 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

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

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.


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