[Bioc-devel] EXTERNAL: Git push error and duplicate commits

On Oct 13, 2017, at 2:59 PM, Matthew Myint <matthewmyint1993 at gmail.com> wrote:

Hi,

Thanks for the explanation! To clarify, the proper step after the
first time you helped restore my repository was to change the Github
branch (with duplicates) to master_deprecated, and switch in the
restored one as master?<div
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Regards
Matthew Myint
Life Science Undergraduate, Year 4
NUS


On Sat, Oct 14, 2017 at 2:49 AM, Turaga, Nitesh
<Nitesh.Turaga at roswellpark.org> wrote:

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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