Subject: [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor).
From: zimoun <[email-masked]>
To: [email-masked]
Cc: zimoun <[email-masked]>
Date: Fri, 21 May 2021 22:21:36 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

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
-- 
2.30.1