[Bioc-devel] EXTERNAL: Git push error and duplicate commits
Hi Matthew,
After closer inspection of ?cytofkit?, it was this commit which caused the duplicates.
commit 4050c245d04af30705245f48931e677a6b4ae159
Merge: 467f659 e6cef6c
Author: Herv? Pag?s <hpages at fredhutch.org>
Date: Wed Sep 20 13:19:45 2017 -0700
Merge branch 'master' of git.bioconductor.org:packages/cytofkit
It was a fetch and merge. So, it means that the GitHub repository hosted (https://github.com/JinmiaoChenLab/cytofkit) did not deprecate the ?master? with duplicate commits by Sept 20th. This was not done till Sept 27th, based on your GitHub logs(https://github.com/JinmiaoChenLab/cytofkit/commits/master_deprecated).
Best,
Nitesh
On Oct 13, 2017, at 2:18 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote: Hi Matthew, I?ll have to fix your branch again, for this I need some time. Do not push any more changes. *When you pull from the upstream (git at git.bioconductor.org), you are not supposed to get any duplicate commits.* If a merge is giving you duplicate commits, it means that you didn?t switch your master branch out. Or forgot to checkout the non-duplicate master. Best, Nitesh
On Oct 13, 2017, at 2:13 PM, Matthew Myint <matthewmyint1993 at gmail.com> wrote: Hi, After you helped me fix my repository, whenever I had updates I would use the steps from https://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/ 1) note down what files needed to be updated in the repository 2) pull from upstream and merge to local branch https://master.bioconductor.org/developers/how-to/git/pull-upstream-changes/ 3) update the needed files in the repository and commit 4) push to both origin and upstream Also, just to clarify, the branch pushing I was referring to was the ?switcheroo? in the link https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenario-6-abandon-changes.md Thanks and regards Matthew Sent from my iPhone On 13 Oct 2017, at 22:35, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:
Hi Matthew, I remember fixing this repository for you a few weeks ago. You cannot push branches to the Bioconductor repository, that is in the FAQ, and documentation. Can you tell me what exactly are the steps you are trying that, you are getting duplicate commits again? Best, Nitesh
On Oct 13, 2017, at 3:39 AM, Matthew Myint <matthewmyint1993 at gmail.com> wrote: Hi, Recently I noticed in hindsight that my repository had duplicate commits, but I missed this during my normal package updating procedures. It was odd that the hook didn't reject these, so I made a clean branch from a commit before the problem occurred and cherry-picking commits to the present state. However, trying to push this to bioconductor git returned an error
remote: FATAL: + refs/heads/master packages/cytofkit c.hao DENIED by fallthru remote: error: hook declined to update refs/heads/master To git.bioconductor.org:packages/cytofkit.git ! [remote rejected] master -> master (hook declined) error: failed to push some refs to 'git at git.bioconductor.org:packages/cytofkit.git'
I've kept the original backed up, and here is the clean branch and back up branch for reference. Here is the link to my repo for additional reference https://github.com/JinmiaoChenLab/cytofkit https://github.com/JinmiaoChenLab/cytofkit/network (network display for easy visualisation) Sorry for the hassle Regards Matthew Myint Life Science Undergraduate, Year 4 NUS
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