[Bioc-devel] Issue with an illegal version bump message when updating an old experiment data package

[Leonardo Collado Torres]

Hi bioc-devel,

Thanks to Nitesh Turaga we were able to get derfinderData back in
sync. Basically:

* We discarded the previous GitHub repo (deleted forever)
* Re-synced via
http://bioconductor.org/developers/how-to/git/maintain-github-bioc/
* The real issue was a bug in the bump version script back in 2014
that bumped the package from 0.99.3 to 0.101.0 instead of 1.1.0
https://github.com/leekgroup/derfinderData/commit/5ea1d9580a4086ecea44cef696679a7e248ff2ab
* Nitesh fixed this manually:
https://github.com/leekgroup/derfinderData/commit/a9ba347501d92ffb2039d01d53159ebe69924b99
* See all new commits: https://github.com/leekgroup/derfinderData/commits/master

Thanks for the input Marcel!

Best,
Leo

On Tue, Sep 25, 2018 at 10:42 PM Ramos Perez, Marcel
<Marcel.RamosPerez using roswellpark.org> wrote:
>
>
> Hi Leonardo,
>
> Keep in mind that GitHub and the Bioconductor git server are two
> different animals.
>
> You should be pushing your changes to the git server as you would with
> software
> packages ( `git using git.bioconductor.org:packages/derfinderData` ).
>
> My guess is that the hook is looking at the version already in the git
> server and
> comparing that to the committed changes (but I could be wrong).
>
> Nitesh can elaborate a bit more on this.
>
> We will look into it on our end.
>
> Regards,
>
> Marcel
>
>
>
>
> On 09/24/2018 10:54 AM, Leonardo Collado Torres wrote:
> > Hi,
> >
> > Marcel Ramos told me a few months ago (July 24, 2018) that experiment
> > data packages are now controlled the same way as software packages via
> > GitHub. Today I finally tried synching the repos following these
> > instructions http://bioconductor.org/developers/how-to/git/sync-existing-repositories/.
> > I had to use the "git merge --allow-unrelated-histories
> > upstream/master" step and resolve 3 small conflicts. It's almost all
> > working well, the step I'm stuck at is:
> >
> > $ git push upstream master
> > Counting objects: 45, done.
> > Delta compression using up to 4 threads.
> > Compressing objects: 100% (38/38), done.
> > Writing objects: 100% (45/45), 5.98 KiB | 1.50 MiB/s, done.
> > Total 45 (delta 25), reused 5 (delta 4)
> > remote: Error: Illegal version bump from '0.115.0' to '0.115.1'. Check
> > remote: http://bioconductor.org/developers/how-to/version-numbering/
> > remote: for details
> > To git.bioconductor.org:packages/derfinderData.git
> >  ! [remote rejected] master -> master (pre-receive hook declined)
> > error: failed to push some refs to
> > 'git using git.bioconductor.org:packages/derfinderData.git'
> >
> > My guess is that the hook is looking at
> > https://github.com/leekgroup/derfinderData/commit/90971f8c8f6b4116d939309942a781bc5f55d9d8
> > and thinks that I'm trying to bump from 0.103.1 to 0.115.1 while in
> > reality the version at
> > http://bioconductor.org/packages/devel/data/experiment/html/derfinderData.html
> > is 0.115.0 (updated in
> > https://github.com/leekgroup/derfinderData/commit/dbf71bbd4418be5a80a6060df8f5f16379a01cb3).
> >
> > Is there something I can do to make this work?
> >
> > GitHub: https://github.com/leekgroup/derfinderData
> > Bioc-devel: http://bioconductor.org/packages/devel/data/experiment/html/derfinderData.html
> >
> > PS I guess that I don't need this file anymore:
> > https://github.com/leekgroup/derfinderData/blob/master/external_data_store.txt
> > nor the currently untracked svn files:
> >
> > $ git status
> > On branch master
> > Your branch is up to date with 'origin/master'.
> >
> > Untracked files:
> >   (use "git add <file>..." to include in what will be committed)
> >
> > data/.svn/
> > inst/extdata/.svn/
> >
> > Best,
> > Leo
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
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