[Bioc-devel] Error pushing changes to upstream

Gaurav Sharma g@h@rm11 @end|ng |rom @|umn|@jh@edu
Wed May 3 15:49:12 CEST 2023


Thanks for your reply. Yes, that's what I did. Here are the commands before `git push`:

> git commit -m 'remove additional description file'
[devel 69c5a8b] remove additional description file
 1 file changed, 45 deletions(-)
 delete mode 100644 DESCRIPTION~

After this when I tried to push these changes upstream, I got the error I shared in the previous email. It is a `pre-receive hook declined` error, so it is possible that the server-side hook has an issue. Perhaps, it is based on the assumption that merge conflict markers are not checked in already, but in this case, they are already in the repo.

Let me know if you need any other information.

From: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Sent: Wednesday, May 3, 2023 9:33 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>; Gaurav Sharma <gsharm11 using alumni.jh.edu>
Subject: Re: [Bioc-devel] Error pushing changes to upstream

Are you able to do a
git commit​
those changes?

Removing l ocally if it is already checked in means you have to do a git rm​ to remove from git repo.


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Gaurav Sharma via Bioc-devel <bioc-devel using r-project.org>
Sent: Wednesday, May 3, 2023 12:33 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Error pushing changes to upstream


I am a developer of the package proejctR. Following the FAQ, I have checked that I have R W access to projectR and my upstream is configured correctly. I get the following error on git push:

Counting objects: 2, done.
Delta compression using up to 12 threads.
Compressing objects: 100% (2/2), done.
Writing objects: 100% (2/2), 235 bytes | 5.00 KiB/s, done.
Total 2 (delta 1), reused 0 (delta 0)
remote: Error: You cannot push without resolving merge conflicts.
remote: Please check the files in the commit pushed to the git-server
remote: for merge conflict markers like '<<<<<<<', '========', '>>>>>>>'.
To git.bioconductor.org:packages/projectR.git
 ! [remote rejected] devel -> devel (pre-receive hook declined)
error: failed to push some refs to 'git using git.bioconductor.org:packages/projectR.git'
I believe this is due to a file named DESCRIPTION~ in the repo upstream (on Bioconductor). The file does have merge conflict markers. However, I removed the file locally, performed a commit, and got the error while git push. That's the only change I did and I didn't do any merge. So, the error is a bit misleading.

I am unable to push the removal of DESCRIPTION~ upstream from my end, and I think this is causing the error. If someone could remove the file and help with this issue, I'll appreciate it.

Thank you.


        [[alternative HTML version deleted]]

Bioc-devel using r-project.org mailing list

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.

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list