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

Matthew Myint matthewmyint1993 at gmail.com
Fri Oct 20 03:56:31 CEST 2017 

Hi Nitesh

I've re-implemented the latest changes with no duplicate commits and
deprecated the problematic branch.

Again, many thanks for your help.
Regards
Matthew Myint
Life Science Undergraduate, Year 4
NUS


On Wed, Oct 18, 2017 at 9:40 PM, Turaga, Nitesh
<Nitesh.Turaga at roswellpark.org> wrote:
> Hi Matthew,
>
> I’ve reset your package to the original clean state. Same place we were last time when this happened.
>
> I encourage you to ask questions on bioc-devel if you are not sure about a certain command, or are facing problems.
>
> Best,
>
> Nitesh
>
>> On Oct 13, 2017, at 3:31 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:
>>
>> 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
>>> id="DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2"><br />
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>>> alt="" width="46" height="29" style="width: 46px; height: 29px;"
>>> /></a></td>
>>>              <td style="width: 470px; padding-top: 12px; color: #41424e;
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>>> href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail"
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>>> </table><a href="#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2" width="1"
>>> height="1"></a></div>
>>> 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
>>>>>>>>
>>>>>>>> _______________________________________________
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