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Re: Move r-{desolve, quadprog, pracma, subplex} from maths.scm to cran.s

From: Ricardo Wurmus
Subject: Re: Move r-{desolve, quadprog, pracma, subplex} from maths.scm to cran.scm
Date: Tue, 10 Dec 2019 09:41:31 +0100
User-agent: mu4e 1.2.0; emacs 26.3

zimoun <address@hidden> writes:

> 1.
> Currently, the file bioconductor.scm contains 4 packages with
> 'cran-uri' and git blames you. :-)
> Well, the 4 commits are:
> : a207bca2ad gnu: r-codedepends: Move from cran to bioconductor.
> : 3a0babacdc gnu: Add r-htscluster.
> : 7ed869f796 gnu: Add r-nbpseq.
> : 80eb01c776 gnu: r-gkmsvm: Move to (gnu packages bioconductor).
> with some comments  as
> --8<---------------cut here---------------start------------->8---
> ;; This is a CRAN package, but it uncharacteristically depends on a
> ;; Bioconductor package
> --8<---------------cut here---------------end--------------->8---
> Do you remember a special motivation?

Yes, the comments say why.  It’s very unusual for a CRAN package to
depend on Bioconductor packages.  Usually, it is the other way around.
I just didn’t want (gnu packages cran) to point to (gnu packages
bioconductor).  A more correct way to deal with this would be put these
outliers in a separate module, or even to ignore this all together until
it becomes a problem.

> 2.
> The second point is that the file statistics.scm contains 227 packages
> and 206 are cran-uri. And the file cran.scm already contains 602
> packages, so it will be almost as python-xyz.scm is. Why not. Then,
> this file statistics.scm will be almost empty and I propose instead to
> populate the files maths.scm, python-xyz.scm.
> What do you think?

statistics.scm was the only thing we had for R in the beginning.  When
it grew and it became apparent that more and more CRAN packages would be
added, I felt that the module became less suitable.

I don’t understand your comment about “maths.scm” and “python-xyz.scm”.
I think it’s good to move CRAN and Bioconductor packages out of
statistics.scm whenever possible.  We can leave the actual statistics
programs there as well as potentially unmovable CRAN packages.

> 3.
> It is a big move. Do you prefer
>  - a commit per package, so more or less 300 commits?
>  - or a commit bioconductor.scm->cran.scm, another
> statistics.scm->cran.scm, bioinformatics.scm->bioconductor.scm and
> bioconductor->bioinformatics.scm, etc.?

I prefer one commit per moved package.  I guess this is not what you
hoped for, but it makes for a more fine-grained log — and it boosts your
commit stats ;)


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