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

From: zimoun
Subject: Re: Move r-{desolve, quadprog, pracma, subplex} from maths.scm to cran.scm
Date: Tue, 10 Dec 2019 13:17:39 +0100


On Tue, 10 Dec 2019 at 09:41, Ricardo Wurmus <address@hidden> wrote:

> > --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.

If I understand well, the policy is: the packages in the file cran.scm
cannot import '(gnu packages bioconductor).

In the file cran.scm, for example the packages r-shiny or r-sankeyd3
do not come from CRAN but directly from Github.
Maybe, we could group all the 6 non-CRAN packages and the 4 CRAN
packages depending on Bioconductor to a unique file.

What do you think?

> > 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.

Sorry, my words was not good enough. I propose to remove the file
statistics.scm by reordering the packages.

> 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.

In the file statistics.scm, once move to cran.scm or bioconductor.scm,
there is few packages. For example 2 packages coming from PyPI and I
propose to move them to the file python-xyz.scm. The other ones could
be moved to the file maths.scm or the unamed (yet) file (see above).

> > 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 ;)

Ahah! I was almost sure you answered that. :-)
Ok, I will.
Be prepared for the storm. ;-)

All the best,

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