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Subject: |
[PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor). |
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Date: |
Fri, 21 May 2021 22:21:36 +0200 |
Hi,
Janitor [1] patch set. It moves Bioconductor packages from (gnu packages
bioinformatics) to (gnu packages bioconductor).
1: <https://lists.gnu.org/archive/html/guix-commits/2020-09/msg00416.html>
To transfer the Copyright, I use:
git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r-<name>
I did my best to preserve the copyright. But I do not guarantee it is
error-free.
Well, in doubt, I have been conservative.
Then, I do:
guix build r-<name> --no-grafts
./pre-inst-env guix build r-<name> --no-grafts --check
To avoid a break, I check with:
for ci in $(git log --format="%H" -51 --reverse);
do
./pre-inst-env guix pull --commit=$ci \
-p /tmp/test-${ci} \
--url=$(pwd) --branch=janitor --disable-authentication
done
and everyting seems fine. At least, "guix pull" should be checked at the end
of the series.
Last, I have checked the imported modules in gnu/packages/bioinformatics.scm.
All should be fine.
Now, I get:
--8<---------------cut here---------------start------------->8---
$ ag 'bioconductor' gnu/packages/bioinformatics.scm
69: #:use-module (gnu packages bioconductor)
11550: (synopsis "Extra base functions for Bioconductor")
11553:provided by Bioconductor packages.")
--8<---------------cut here---------------end--------------->8---
which ends the move, I guess. Except the package r-rcurl in
gnu/packages/statistics.scm, let as an exercise for the reader. ;-)
On a side note about the Copyright lines, I did:
git blame --date=format:"%Y)" gnu/packages/bioinformatics.scm \
| cut -d')' -f1 | cut -d'(' -f2 | sed 's/ //g' \
| sort | uniq -c
and it is possible that there is some "mistake", FWIW.
All the best,
simon
zimoun (50):
gnu: r-genomicalignments: Move to (gnu packages bioconductor).
gnu: r-rtracklayer: Move to (gnu packages bioconductor).
gnu: r-genomicfeatures: Move to (gnu packages bioconductor).
gnu: r-topgo: Move to (gnu packages bioconductor).
gnu: r-bsgenome: Move to (gnu packages bioconductor).
gnu: r-msnid: Move to (gnu packages bioconductor).
gnu: r-msnbase: Move to (gnu packages bioconductor).
gnu: r-samr: Move to (gnu packages bioconductor).
gnu: r-impute: Move to (gnu packages bioconductor).
gnu: r-seqpattern: Move to (gnu packages bioconductor).
gnu: r-go-db: Move to (gnu packages bioconductor).
gnu: r-genomation: Move to (gnu packages bioconductor).
gnu: r-genomationdata: Move to (gnu packages bioconductor).
gnu: r-pcamethods: Move to (gnu packages bioconductor).
gnu: r-mzid: Move to (gnu packages bioconductor).
gnu: r-aroma-light: Move to (gnu packages bioconductor).
gnu: r-deseq: Move to (gnu packages bioconductor).
gnu: r-edaseq: Move to (gnu packages bioconductor).
gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor).
gnu: r-annotationhub: Move to (gnu packages bioconductor).
gnu: r-fastseg: Move to (gnu packages bioconductor).
gnu: r-affy: Move to (gnu packages bioconductor).
gnu: r-keggrest: Move to (gnu packages bioconductor).
gnu: r-gage: Move to (gnu packages bioconductor).
gnu: r-complexheatmap: Move to (gnu packages bioconductor).
gnu: r-genomicfiles: Move to (gnu packages bioconductor).
gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor).
gnu: r-organismdbi: Move to (gnu packages bioconductor).
gnu: r-affyio: Move to (gnu packages bioconductor).
gnu: r-vsn: Move to (gnu packages bioconductor).
gnu: r-biovizbase: Move to (gnu packages bioconductor).
gnu: r-ensembldb: Move to (gnu packages bioconductor).
gnu: r-mzr: Move to (gnu packages bioconductor).
gnu: r-protgenerics: Move to (gnu packages bioconductor).
gnu: r-sva: Move to (gnu packages bioconductor).
gnu: r-motifrg: Move to (gnu packages bioconductor).
gnu: r-seqlogo: Move to (gnu packages bioconductor).
gnu: r-zlibbioc: Move to (gnu packages bioconductor).
gnu: r-rhtslib: Move to (gnu packages bioconductor).
gnu: r-bamsignals: Move to (gnu packages bioconductor).
gnu: r-rcas: Move to (gnu packages bioconductor).
gnu: r-mutationalpatterns: Move to (gnu packages bioconductor).
gnu: r-tximport: Move to (gnu packages bioconductor).
gnu: r-rhdf5filters: Move to (gnu packages bioconductor).
gnu: r-annotationfilter: Move to (gnu packages bioconductor).
gnu: r-rhdf5: Move to (gnu packages bioconductor).
gnu: r-chipseq: Move to (gnu packages bioconductor).
gnu: r-copyhelper: Move to (gnu packages bioconductor).
gnu: r-copywriter: Move to (gnu packages bioconductor).
gnu: r-methylkit: Move to (gnu packages bioconductor).
gnu/packages/bioconductor.scm | 1826 +++++++++++++++++++++++++++++--
gnu/packages/bioinformatics.scm | 1645 ----------------------------
gnu/packages/cran.scm | 30 -
3 files changed, 1749 insertions(+), 1752 deletions(-)
base-commit: bd382fae71d899e243e81688bf5baed26171f2ea
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2.30.1
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