| Message ID | 20210315180714.8233-1-zimon.toutoune@gmail.com |
|---|---|
| Headers | show |
| Series | Move some Bioconductor packages to (gnu packages bioconductor). | expand |
Hi, > 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.
On Mon, Mar 15, 2021 at 11:33:11PM +0100, Ricardo Wurmus wrote: > Hi, > > > 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.
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
zimoun <zimon.toutoune@gmail.com> writes: > 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? The point of having (gnu packages cran) and (gnu packages bioconductor) be separate modules is to separate independent packages. I’d like to keep it that way and not let (gnu packages cran) depend on (gnu packages bioconductor).
Hi, On Tue, 16 Mar 2021 at 14:20, Ricardo Wurmus <rekado@elephly.net> wrote: > zimoun <zimon.toutoune@gmail.com> writes: > > > 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? > > The point of having (gnu packages cran) and (gnu packages bioconductor) > be separate modules is to separate independent packages. > > I’d like to keep it that way and not let (gnu packages cran) depend on > (gnu packages bioconductor). Therefore, the fix is to move the CRAN r-bisquerna and r-absfiltergsea packages from (gnu packages cran) to (gnu packages bioconductor) because they depend on the Bioconductor package r-biobase (and r-limma). Right? How do I proceed? Submit a patch moving these 2 packages and then another patch reverting the revert? Thanks, simon
zimoun <zimon.toutoune@gmail.com> writes: > Hi, > > On Tue, 16 Mar 2021 at 14:20, Ricardo Wurmus <rekado@elephly.net> wrote: >> zimoun <zimon.toutoune@gmail.com> writes: >> >> > 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? >> >> The point of having (gnu packages cran) and (gnu packages bioconductor) >> be separate modules is to separate independent packages. >> >> I’d like to keep it that way and not let (gnu packages cran) depend on >> (gnu packages bioconductor). > > Therefore, the fix is to move the CRAN r-bisquerna and r-absfiltergsea > packages from (gnu packages cran) to (gnu packages bioconductor) > because they depend on the Bioconductor package r-biobase (and > r-limma). Right? Correct. We don’t want any CRAN packages to depend on Bioconductor things. When this is unavoidable, though, we move them to (gnu packages bioconductor) with a comment. > How do I proceed? Submit a patch moving these 2 packages and then > another patch reverting the revert? Sounds good. (You could do this all in the same issue.)
On Tue, 16 Mar 2021 at 17:08, Ricardo Wurmus <rekado@elephly.net> wrote: > > Therefore, the fix is to move the CRAN r-bisquerna and r-absfiltergsea > > packages from (gnu packages cran) to (gnu packages bioconductor) > > because they depend on the Bioconductor package r-biobase (and > > r-limma). Right? > > Correct. We don’t want any CRAN packages to depend on Bioconductor > things. When this is unavoidable, though, we move them to (gnu packages > bioconductor) with a comment. Ok. > > How do I proceed? Submit a patch moving these 2 packages and then > > another patch reverting the revert? > > Sounds good. (You could do this all in the same issue.) By the same issue, do you mean the same guix-patches number? Or the same commit? Cheers, simon
zimoun <zimon.toutoune@gmail.com> writes: >> > How do I proceed? Submit a patch moving these 2 packages and then >> > another patch reverting the revert? >> >> Sounds good. (You could do this all in the same issue.) > > By the same issue, do you mean the same guix-patches number? Or the > same commit? I meant the same guix-patches issue number; separate commits.
Hi Ricardo,
On Tue, 16 Mar 2021 at 23:04, Ricardo Wurmus <rekado@elephly.net> wrote:
> I meant the same guix-patches issue number; separate commits.
Done in v2. I have double-checked but who knows. :-)
Thanks,
simon
Hi, Janitor [1] patch set. It moves Bioconductor packages from (gnu packages bioinformatics) to (gnu packages bioconductor). Far to be complete; still 4 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-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). gnu/packages/bioconductor.scm | 305 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 305 -------------------------------- 2 files changed, 305 insertions(+), 305 deletions(-) base-commit: 266d55dc3080475544bf45e72359c9b9bbcecd53