[Bioc-devel] Fwd: Git error when pushing to bioconductor

[Turaga, Nitesh]

Forwarding to bioc-devel as it is a useful topic in git branch divergence.

Begin forwarded message:

From: ni41435_ca <nitesh.turaga using roswellpark.org<mailto:nitesh.turaga using roswellpark.org>>
Subject: Re: [Bioc-devel] Git error when pushing to bioconductor
Date: June 22, 2018 at 3:44:50 PM EDT
To: "Kangeyan, Divy" <divyswar01 using g.harvard.edu<mailto:divyswar01 using g.harvard.edu>>

Hi Divy


You haven’t pushed to the remote branch since https://github.com/aryeelab/scmeth/commit/77854c66812bc8341f1aa722023ac371982066af.

And after that the histories have diverged completely. The Bioconductor version has (1737d8609f78099002841a9a78266bf3e6535146), whereas the GitHub version goes into the commit (8040210d9327a1de81861d5af2aae69c62f434c0).

One way to solve this is to follow these steps on your local machine.

## Make a backup of your current master branch
git branch master_backup

## rename your current master branch
git branch -M master_deprecated

## checkout bioconductors master
git checkout -b master upstream/master (this only works if your remotes are correct)

## Now cherry pick all the commits you want from your master backup branch on to the proper version of master
git cherry-pick <commit id from master_backup branch>

( you can check the log of your master_backup by using `git log master_backup`)


Then once you have gotten all the commits onto the new master branch in the correct way, try to push to both Github and Bioconductor.

You should be able to force push to your GitHub, but you cannot to Bioconductor. Since it is a traced checkout of the bioconductor master branch, it will not require a force push.

Try that and let me know if it helps.

Best,

Nitesh



On Jun 22, 2018, at 3:28 PM, Kangeyan, Divy <divyswar01 using g.harvard.edu<mailto:divyswar01 using g.harvard.edu>> wrote:

After digging into the git history, I found that my current remote bioconductor branch is with 1737d860 as the last commit ID. I couldn't find this ID in my local commit history or in the github commit history. Since then I have made some changes in my local directory and it is in sync with the github commits. But for some reason I couldn't push any changes to the remote bioconductor branch.

Divy


On Fri, Jun 22, 2018 at 1:04 PM, Kangeyan, Divy <divyswar01 using g.harvard.edu<mailto:divyswar01 using g.harvard.edu>> wrote:
I think I am following those steps to update the local changes and resolve the conflicts. Yes, I do have a Github version of the  package: https://github.com/aryeelab/scmeth

The file that is causing the issue is called qcReport.Rmd. It is in the inst folder.

Divy

On Fri, Jun 22, 2018 at 12:57 PM, Turaga, Nitesh <Nitesh.Turaga using roswellpark.org<mailto:Nitesh.Turaga using roswellpark.org>> wrote:
I don’t understand how that can happen. Are you following http://bioconductor.org/developers/how-to/git/resolve-conflicts/? And these are the steps you have taken to update your local branch (http://bioconductor.org/developers/how-to/git/pull-upstream-changes/)?

Can you show me the file which you fixed conflicts for?  Do you have a Github version of your package?

Best,

Nitesh

On Jun 22, 2018, at 12:54 PM, Kangeyan, Divy <divyswar01 using g.harvard.edu<mailto:divyswar01 using g.harvard.edu>> wrote:

I fixed the conflict and then pushed the changes to the origin and upstream/master. I am getting the same error when push to upstream/master.

Divy

On Fri, Jun 22, 2018 at 12:40 PM, Turaga, Nitesh <Nitesh.Turaga using roswellpark.org<mailto:Nitesh.Turaga using roswellpark.org>> wrote:
Fix the conflict.



On Jun 22, 2018, at 12:38 PM, Kangeyan, Divy <divyswar01 using g.harvard.edu<mailto:divyswar01 using g.harvard.edu>> wrote:

<git_pull.png>



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--
Divy Kangeyan
PhD Student
Department of Biostatistics
Harvard T.H. Chan School of Public Health



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.



--
Divy Kangeyan
PhD Student
Department of Biostatistics
Harvard T.H. Chan School of Public Health



--
Divy Kangeyan
PhD Student
Department of Biostatistics
Harvard T.H. Chan School of Public Health




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.
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