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bug#54787: importer Bioconductor: no tarball, only Git
From: |
Ricardo Wurmus |
Subject: |
bug#54787: importer Bioconductor: no tarball, only Git |
Date: |
Thu, 14 Apr 2022 15:57:25 +0200 |
User-agent: |
mu4e 1.6.10; emacs 28.0.50 |
zimoun <zimon.toutoune@gmail.com> writes:
> On Thu, 14 Apr 2022 at 13:43, Ricardo Wurmus <rekado@elephly.net> wrote:
>
>> We probably should *not* use RELEASE_3_14 (or whatever) as the commit,
>> though, because that is a moving target. We need to resolve to the
>> actual commit and use its hash.
>>
>> I wonder how the updater would need to be changed. It would need to
>> know about the release branch and look for new commits in that branch
>> only.
>
> To be honest, I have not checked the Bioconductor documentation about
> their Git repo structure. What I see is:
>
> $ git clone https://git.bioconductor.org/packages/CHETAH
> $ cd CHETAH
> $ git branch -av
> * master 5d5f5df [origin/master] Pass serialized S4
> instances thru updateObject()
> remotes/origin/HEAD -> origin/master
> remotes/origin/RELEASE_3_10 063de2d bump x.y.z version to even y prior to
> creation of RELEASE_3_10 branch
> remotes/origin/RELEASE_3_11 701ca7f bump x.y.z version to even y prior to
> creation of RELEASE_3_11 branch
> remotes/origin/RELEASE_3_12 cd3dd78 bump x.y.z version to even y prior to
> creation of RELEASE_3_12 branch
> remotes/origin/RELEASE_3_13 1eacdb8 bump x.y.z version to even y prior to
> creation of RELEASE_3_13 branch
> remotes/origin/RELEASE_3_14 03295c9 bump x.y.z version to even y prior to
> creation of RELEASE_3_14 branch
> remotes/origin/RELEASE_3_9 22b53f2 version bump
> remotes/origin/master 5d5f5df Pass serialized S4 instances thru
> updateObject()
>
>
> Do we follow ’master’? Is it a mirror of what Bioconductor names their
> 3.14 release?
We should not follow “master”. That’s the development branch. We
should follow the current release branch.
> My guess was that RELEASE_3_14 mirrors their 3.14 release.
Correct.
>>> Well, I am also in favor to break the API and move %bioconductor-version
>>> and %bioconductor-url to (guix build-system r). WDYT? It would
>>> simplify some things (#36805 and #39885), I guess.
>>
>> We tried this before and we couldn’t do this because of a circular
>> reference.
>
> Well, I have something that works. So I do not know if this circular
> reference is still there.
If “make as-derivation” does not fail it is probably okay.
>> That’s because the importer doesn’t let us specify a different branch.
>> We should add that, but it’s strictly separate from the migration we’re
>> about to embark on.
>
> I am not familiar with the updater (guix refresh -u). My plan is:
>
> 1. Add bioconductor-git-reference
> 2. Adapt the bioconductor importer.
> 3. Updater?
The updater is closely connected to the importer. It just needs to be
told how it can find new releases.
> The question is: do we have to include the migration in the updater? Or
> do we do the migration by custom scripts?
We can do the migration manually. But if we end up with a broken
updater I won’t be able to update Bioconductor packages in bulk; that
would be a serious problem for future maintenance.
> Note that, because we do not support shallow clones, the complete
> sources will be a bit bigger; since they contain all the Bioconductor
> history of all the packages.
Doesn’t Guile-Git support shallow clones? In any case, this should not
be an obstacle for us. Ensuring long-term reproducibility is more
important than space savings.
--
Ricardo
- bug#54787: importer Bioconductor: no tarball, only Git, zimoun, 2022/04/08
- bug#54787: importer Bioconductor: no tarball, only Git, Ricardo Wurmus, 2022/04/11
- bug#54787: importer Bioconductor: no tarball, only Git, zimoun, 2022/04/12
- bug#54787: importer Bioconductor: no tarball, only Git, Ricardo Wurmus, 2022/04/14
- bug#54787: importer Bioconductor: no tarball, only Git, zimoun, 2022/04/14
- bug#54787: importer Bioconductor: no tarball, only Git,
Ricardo Wurmus <=
- bug#54787: importer Bioconductor: no tarball, only Git, zimoun, 2022/04/14
- bug#54787: importer Bioconductor: no tarball, only Git, Maxime Devos, 2022/04/14