[bug#43345] [PATCH 00/12] Move some CRAN packages to (gnu packages cran).

[zimoun <zimon.toutoune@gmail.com>]

Dear,

Some clean up leading the recent discussion [1].  Now, the only remaining
'cran-uri' are from (gnu packages statistics).  Modulo maybe some packages
using "bad" uri, e.g., from r-qtl:

--8<---------------cut here---------------start------------->8---
    (uri (string-append "mirror://cran/src/contrib/qtl_"
                        version ".tar.gz"))
--8<---------------cut here---------------end--------------->8---

To ease the Copyright transfer between files, I used:

  git log --grep=<package-name>
  git log --date=format:"%Y" --format="%ad %an" \
      -- gnu/packages/<file>.scm | sort | uniq -c

After each move, I run:

  make
  ./pre-env-inst guix build <package-name>
  ./pre-env-inst guix build <package-name> --no-grafts --check

to check that everything is fine.  And at the end of all the move, I run:

  make as-derivation

to verify that "guix pull" is not broken by something.  (Well, I failed to use
the regular ./pre-env-inst guix pull --branch=my-stuff --url=$PWD -p /tmp/new
because of the "new" authentication, another story.)

Last, I have not carefully checked the imported modules, so it could be
possible to perhaps remove 1 or 2 #:use-module (gnu packages <useless>) from
gnu/packages/bioinformatics.scm.

[1] https://lists.gnu.org/archive/html/guix-commits/2020-09/msg00416.html

All the best,
simon

zimoun (12):
  gnu: r-codedepends: Comment why is in bioconductor.scm.
  gnu: r-adaptivesparsity: Move to (gnu packages cran).
  gnu: r-diffusionmap: Move to (gnu packages cran).
  gnu: r-igraph: Move to (gnu packages cran).
  gnu: r-qtl: Move to (gnu packages cran).
  gnu: r-qtl2: Move to (gnu packages cran).
  gnu: r-seqminer: Move to (gnu packages cran).
  gnu: r-maldiquant: Move to (gnu packages cran).
  gnu: r-seurat: Move to (gnu packages cran).
  gnu: r-phangorn: Move to (gnu packages cran).
  gnu: r-diversitree: Move to (gnu packages cran).
  gnu: r-absfiltergsea: Move to (gnu packages cran).

 gnu/packages/bioconductor.scm     |   1 +
 gnu/packages/bioinformatics.scm   | 250 ---------------------
 gnu/packages/cran.scm             | 346 ++++++++++++++++++++++++++++++
 gnu/packages/graph.scm            |  57 -----
 gnu/packages/machine-learning.scm |  35 ---
 5 files changed, 347 insertions(+), 342 deletions(-)


base-commit: 24e37fbbc4d7a5a4792c57f97f1f280d3ed36e01
-- 
2.28.0