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Subject: |
[PATCH 00/12] Move some CRAN packages to (gnu packages cran). |
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Date: |
Fri, 11 Sep 2020 20:05:27 +0200 |
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
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--- Begin Message ---
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Subject: |
Re: [bug#43345] [PATCH 00/12] Move some CRAN packages to (gnu packages cran). |
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Date: |
Fri, 11 Sep 2020 22:07:46 +0200 |
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User-agent: |
mu4e 1.4.13; emacs 27.1 |
Hi simon,
thank you for this janitorial work!
> 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---
I fixed that URL (and a few more things that became obvious during the
move).
> 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
Excellent! Thank you for being so dilligent. For some reason you
missed the import of (gnu packages xml) after the move of r-igraph. I
added it. I also updated the commit messages for consistency in
punctuation (sorry for being picky).
Pushed to the “master” branch with commit 8458490bc2.
Thanks again!
--
Ricardo
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