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Re: branch master updated: gnu: Add r-loomr.

From: Ricardo Wurmus
Subject: Re: branch master updated: gnu: Add r-loomr.
Date: Thu, 10 Sep 2020 12:38:41 +0200
User-agent: mu4e 1.4.13; emacs 27.1

Roel Janssen <> writes:

>> > commit 1f56ec08af704bdc7aa3e143bf5ce351c5306dea
>> > Author: Roel Janssen <>
>> > AuthorDate: Wed Sep 9 16:56:02 2020 +0200
>> > 
>> >     gnu: Add r-loomr.
>> >     
>> >     * gnu/packages/bioinformatics.scm (r-loomr): New variable.
>> This is not free software.  See
> Oh shoot. I'm sorry I didn't see this discussion!

It’s really not obvious.  I know because it happened to me too.  In 2018
I added r-loomr with commit fab43c6b84635200070c708d4220132be18dd239.
Then in 2019 I removed it with commit
bc70516bbae8a6388f3ed19008d3e10efd1577a7 after noticing that the author
only used GPL in the DESCRIPTION file to stop the CRAN tools from

It’s definitely unusual and very easy to miss.

>> Aside from this, I would like to say two things:
>> >  gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
>> Let’s please not add R packages to (gnu packages bioinformatics) when
>> it
>> can be avoided.  (In this case there’s no CRAN package, so it’s
>> fine.)
> Where would I add a non-CRAN and non-Bioconductor package to?  Perhaps
> this situation won't occur again, and should raise a flag, because I
> think I've never had this case before.

We don’t have any good place for those packages.  It would be good to
have a dumping ground for packages like that, and for those that are on
CRAN but unusually depend on Bioconductor packages.

> I will default to submitting patches to guix-patches again.  I thought
> it was trivial enough to just push.  My mistake.

I’d say if it’s on CRAN you can go ahead and push directly (after
running “guix lint” to catch some obvious mistakes).  Bioconductor
packages need a little extra care because they are sometimes playing
loose with licenses and included third-party code; but if you feel
you’ve checked things carefully then you can also push those directly.

For third-party R packages we don’t benefit from even the little bit of
quality control that CRAN and Bioconductor impose, so we need to be
extra careful.  There it helps to send patches to guix-patches and push
them after some time.


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