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 at 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] Issue with an illegal version bump message when updating an old experiment data package
2 messages · Leonardo Collado Torres, Ramos Perez, Marcel
1 day later
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 at 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 at 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 at 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.