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Re: bioinformatics.scm vs bioconductor.scm ?

From: Ricardo Wurmus
Subject: Re: bioinformatics.scm vs bioconductor.scm ?
Date: Tue, 18 Dec 2018 23:45:48 +0100
User-agent: mu4e 1.0; emacs 26.1


> Is the bioconductor importer usable from `guix import` ?

yes.  You may encounter minor problems when using the recursive
bioconductor importer, as it may try to look up CRAN packages on

> This package is on Bioconductor:

I’d do

    ./pre-inst-env guix import cran -a bioconductor -r flowCore

This fails because it wants corpcor from CRAN.  So we do:

    ./pre-inst-env guix import cran -r corpcor

We dump the result (with minor changes) in (gnu packages cran) and try
again to import flowCore.  This time it succeeds.

> Hum, the package BiocGenerics needs the version >= 0.1.14, and it is
> not defined in the package.

We have r-biocgenerics 0.28.0 in gnu/packages/bioinformatics.scm.
That’s one of the packages that should move eventually.

> Then, the package grDevices, graphics, methods, stats, stats4 are
> required (see bioconductor webpage) but not defined elsewhere. Is it
> good ?

These are all default packages that are part of R itself.  The importer
skips them.

> What is the convention about license ?
> (license name) or (license license:name)

This depends on the target module.  cran.scm, bioinformatics.scm, and
bioconductor.scm all use the “license:” prefix.  web.scm on the other
hand uses the “l:” prefix.  Take a look at the #:use-module clause at
the top of the module.


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