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.ramospe...@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 ( `g...@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 > > 'g...@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@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
