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: Tue, 18 Dec 2018 23:45:48 +0100 [thread overview]
Message-ID: <87mup2tpwj.fsf@elephly.net> (raw)
In-Reply-To: <CAJ3okZ3_4tzHHYO5aEOv=wh7qQnzb_6ZEHe_GvdBTbbpqi+v_A@mail.gmail.com>
Hi,
> 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
Bioconductor.
> This package is on Bioconductor:
> https://bioconductor.org/packages/release/bioc/html/flowCore.html
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.
--
Ricardo
next prev parent reply other threads:[~2018-12-18 22:46 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
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 [this message]
2018-12-20 8:46 ` Ricardo Wurmus
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