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

[Turaga, Nitesh]

Yes. That is correct. 


> 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: Hervé Pagès <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
>>>>>> 
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>> 
>>>>> 
>>>>> 
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