From: zimoun <zimon.toutoune@gmail.com>
To: Leo Famulari <leo@famulari.name>
Cc: Ricardo Wurmus <rekado@elephly.net>, 47171@debbugs.gnu.org
Subject: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).
Date: Tue, 16 Mar 2021 13:27:01 +0100 [thread overview]
Message-ID: <CAJ3okZ0+tMAOQtpL+1FN5x6dNs10gOUGGrtRrXBj3kZphgU2wg@mail.gmail.com> (raw)
In-Reply-To: <YE/0IpB2HTm8XwWT@jasmine.lan>
Hi Leo,
On Tue, 16 Mar 2021 at 00:56, Leo Famulari <leo@famulari.name> wrote:
> On Mon, Mar 15, 2021 at 11:33:11PM +0100, Ricardo Wurmus wrote:
> > > zimoun (10):
> > > gnu: r-limma: Move to (gnu packages bioconductor).
> > > gnu: r-xvector: Move to (gnu packages bioconductor).
> > > gnu: r-genomicranges: Move to (gnu packages bioconductor).
> > > gnu: r-biobase: Move to (gnu packages bioconductor).
> > > gnu: r-annotationdbi: Move to (gnu packages bioconductor).
> > > gnu: r-biomart: Move to (gnu packages bioconductor).
> > > gnu: r-biocparallel: Move to (gnu packages bioconductor).
> > > gnu: r-biostrings: Move to (gnu packages bioconductor).
> > > gnu: r-rsamtools: Move to (gnu packages bioconductor).
> > > gnu: r-delayedarray: Move to (gnu packages bioconductor).
> >
> > Thanks, I’ve pushed them all.
>
> These commits caused `guix pull` to fail, as described here:
>
> https://git.savannah.gnu.org/cgit/guix.git/commit/?id=8ec0ca8faff62f19426f22aeb1bd59a8950ca05a
>
> I think we just needed to import the bioconductor module in the cran
> module, but I wasn't sure so I reverted them in order to fix the problem
> quickly.
Sorry for the annoyance. I did "make as-derivation" and it reports
nothing. But indeed, "./pre-inst-env guix pull -p /tmp/new
--url=$(pwd) --disable-authentication --branch=test" breaks.
I do not know if I do something wrong (run make in a worktree for the branch).
Well, thanks for the report and I confirm that adding the bioconductor
import in cran fixes "guix pull". But in my memories, this import
was adding circular dependency. Ricardo, WDYT?
Cheers,
simon
next prev parent reply other threads:[~2021-03-16 12:29 UTC|newest]
Thread overview: 24+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-03-15 18:07 [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor) zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 01/10] gnu: r-limma: Move " zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 02/10] gnu: r-xvector: " zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 03/10] gnu: r-genomicranges: " zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 04/10] gnu: r-biobase: " zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 05/10] gnu: r-annotationdbi: " zimoun
2021-03-15 18:09 ` [bug#47171] [PATCH 06/10] gnu: r-biomart: " zimoun
2021-03-15 18:09 ` [bug#47171] [PATCH 07/10] gnu: r-biocparallel: " zimoun
2021-03-15 18:09 ` [bug#47171] [PATCH 08/10] gnu: r-biostrings: " zimoun
2021-03-15 18:09 ` [bug#47171] [PATCH 09/10] gnu: r-rsamtools: " zimoun
2021-03-15 18:09 ` [bug#47171] [PATCH 10/10] gnu: r-delayedarray: " zimoun
2021-03-15 22:33 ` bug#47171: [PATCH 00/10] Move some Bioconductor packages " Ricardo Wurmus
2021-03-15 23:56 ` [bug#47171] " Leo Famulari
2021-03-16 12:27 ` zimoun [this message]
2021-03-16 13:20 ` Ricardo Wurmus
2021-03-16 13:30 ` zimoun
2021-03-16 16:08 ` Ricardo Wurmus
2021-03-16 16:36 ` zimoun
2021-03-16 22:04 ` Ricardo Wurmus
2021-03-17 20:15 ` zimoun
2021-03-17 20:14 ` [bug#47171] [PATCH v2 1/3] gnu: r-bisquerna: Move " zimoun
2021-03-17 20:14 ` [bug#47171] [PATCH v2 2/3] gnu: r-absfiltergsea: " zimoun
2021-03-17 20:14 ` [bug#47171] [PATCH v2 3/3] Revert "Revert some commits that caused `guix pull` to fail." zimoun
2021-03-31 19:29 ` bug#47171: [PATCH v2 1/3] gnu: r-bisquerna: Move to (gnu packages bioconductor) Ricardo Wurmus
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