mbox series

[bug#47156,00/10] Move some Bioconductor packages to (gnu packages bioconductor).

Message ID 20210315125800.30246-1-zimon.toutoune@gmail.com
Headers show
Series Move some Bioconductor packages to (gnu packages bioconductor). | expand

Message

Simon Tournier March 15, 2021, 12:58 p.m. UTC 
Hi,

Janitor [1] patch set.  It moves Bioconductor packages from (gnu packages
bioinformatics) to (gnu packages bioconductor).  Far to be complete; still 5
pacth set like this one are coming...

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>

Then, after the move, I run:

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

and at the end of the series, I run:

    make as-derivation

to check that "guix pull" is not broken; just in case.

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

All the best,
simon

zimoun (10):
  gnu: r-grohmm: Move to (gnu packages bioconductor).
  gnu: r-biocviews: Move to (gnu packages bioconductor).
  gnu: r-biocstyle: Move to (gnu packages bioconductor).
  gnu: r-bioccheck: Move to (gnu packages bioconductor).
  gnu: r-s4vectors: Move to (gnu packages bioconductor).
  gnu: r-iranges: Move to (gnu packages bioconductor).
  gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor).
  gnu: r-genomeinfodb: Move to (gnu packages bioconductor).
  gnu: r-edger: Move to (gnu packages bioconductor).
  gnu: r-variantannotation: Move to (gnu packages bioconductor).

 gnu/packages/bioconductor.scm   | 303 +++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 307 --------------------------------
 2 files changed, 303 insertions(+), 307 deletions(-)


base-commit: 1ed435bf394eee1a6cd9c354efb405920c212f0e

Comments

Ricardo Wurmus March 15, 2021, 1:09 p.m. UTC | #1 
zimoun <zimon.toutoune@gmail.com> writes:
>
> Janitor [1] patch set.  It moves Bioconductor packages from (gnu packages
> bioinformatics) to (gnu packages bioconductor).  Far to be complete; still 5
> pacth set like this one are coming...

Thank you, I applied it (last commit is
bf612ead766ee5afcdccd7c8ab003b791ecea9df).