Dear admin, I am an author of a Bioconductor package (TSCAN) and recently I made a mistake pushing a problematic version of the software to Bioconductor. I wonder if there is a way to revert back to the previous working version? Thanks! Best, Jason -- Zhicheng Ji, PhD. Assistant Professor Department of Biostatistics and Bioinformatics Duke University School of Medicine 2424 Erwin Road, Suite 1102 Hock Plaza Box 2721 Durham, NC 27710, USA
[Bioc-devel] reverting to a previous version
4 messages · Jason Ji, Hervé Pagès
Hi Jason,
On 19/10/2022 19:10, Jason Ji wrote:
Dear admin, I am an author of a Bioconductor package (TSCAN) and recently I made a mistake pushing a problematic version of the software to Bioconductor. I wonder if there is a way to revert back to the previous working version?
Yes but only for the master branch (BioC 3.16). The RELEASE_3_15 branch got frozen recently and can no longer be touched. Also package versions can only go up. Note that the current devel version of? TSCAN (1.35.1) never got published (i.e. it didn't propagate), so, technically, you won't need to bump the version after you fix the package. Even though it wouldn't hurt to do so (i.e. to bump to 1.35.2). Cheers, H.
Thanks! Best, Jason -- Zhicheng Ji, PhD. Assistant Professor Department of Biostatistics and Bioinformatics Duke University School of Medicine 2424 Erwin Road, Suite 1102 Hock Plaza Box 2721 Durham, NC 27710, USA [[alternative HTML version deleted]]
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Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com
Thanks Herv?, I am sorry I am not familiar with the Bioconductor git system. Could you please advise the code I should use to revert to the last working version? Thanks! Best, Jason -- Zhicheng Ji, PhD. Assistant Professor Department of Biostatistics and Bioinformatics Duke University School of Medicine 2424 Erwin Road, Suite 1102 Hock Plaza Box 2721 Durham, NC 27710, USA On Wed, Oct 19, 2022 at 10:29 PM Herv? Pag?s <hpages.on.github at gmail.com> wrote:
Hi Jason, On 19/10/2022 19:10, Jason Ji wrote:
Dear admin, I am an author of a Bioconductor package (TSCAN) and recently I made a mistake pushing a problematic version of the software to Bioconductor. I wonder if there is a way to revert back to the previous working version?
Yes but only for the master branch (BioC 3.16). The RELEASE_3_15 branch got frozen recently and can no longer be touched. Also package versions can only go up. Note that the current devel version of TSCAN (1.35.1) never got published (i.e. it didn't propagate), so, technically, you won't need to bump the version after you fix the package. Even though it wouldn't hurt to do so (i.e. to bump to 1.35.2). Cheers, H.
Thanks!
Best,
Jason
--
Zhicheng Ji, PhD.
Assistant Professor
Department of Biostatistics and Bioinformatics
Duke University School of Medicine
2424 Erwin Road, Suite 1102 Hock Plaza Box 2721
Durham, NC 27710, USA
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com
On 19/10/2022 19:48, Jason Ji wrote:
Thanks Herv?, I am sorry I am not familiar with the Bioconductor git system. Could you please advise the code I should use to revert to the last working version? Thanks!
I'm not a git expert so maybe others have a better way to do this. I would just identify the commit you want to revert (the fact that all the recent commit messages are "commit" won't necessarily help), then revert it with: ? git revert <commit> If you need to revert more than 1 commit, revert them in reverse chronological order. This is just standard git stuff. The only part that is specific to Bioconductor is that you need to finish the sequence with an additional commit that bumps the version to 1.35.2. Hope this helps, H.
Best,
Jason
--
Zhicheng Ji, PhD.
Assistant Professor
Department of Biostatistics and Bioinformatics
Duke University School of Medicine
2424 Erwin Road, Suite 1102 Hock Plaza Box 2721
Durham, NC 27710, USA
On Wed, Oct 19, 2022 at 10:29 PM Herv? Pag?s
<hpages.on.github at gmail.com> wrote:
Hi Jason,
On 19/10/2022 19:10, Jason Ji wrote:
> Dear admin,
>
> I am an author of a Bioconductor package (TSCAN) and recently I
made a
> mistake pushing a problematic version of the software to
Bioconductor. I
> wonder if there is a way to revert back to the previous working
version?
Yes but only for the master branch (BioC 3.16). The RELEASE_3_15
branch
got frozen recently and can no longer be touched.
Also package versions can only go up. Note that the current devel
version of? TSCAN (1.35.1) never got published (i.e. it didn't
propagate), so, technically, you won't need to bump the version after
you fix the package. Even though it wouldn't hurt to do so (i.e.
to bump
to 1.35.2).
Cheers,
H.
>
> Thanks!
>
>
> Best,
> Jason
>
> --
> Zhicheng Ji, PhD.
> Assistant Professor
> Department of Biostatistics and Bioinformatics
> Duke University School of Medicine
> 2424 Erwin Road, Suite 1102 Hock Plaza Box 2721
> Durham, NC 27710, USA
>
>? ? ? ?[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Herv? Pag?s
Bioconductor Core Team
hpages.on.github at gmail.com
Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com [[alternative HTML version deleted]]