[Bioc-devel] Duplicate commit error when pushing to annotatr upstream/master

Hello,

I?m running into the following error when trying to push some changes to annotatr upstream/master:
rcavalca$ git push upstream master
Counting objects: 6, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (6/6), done.
Writing objects: 100% (6/6), 854 bytes | 854.00 KiB/s, done.
Total 6 (delta 5), reused 0 (delta 0)
remote: Error: duplicate commits.
remote: 
remote: There are duplicate commits in your commit history, These cannot be
remote: pushed to the Bioconductor git server. Please make sure that this is
remote: resolved.
remote: 
remote: Take a look at the documentation to fix this,
remote: https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
remote: particularly, point #8 (force Bioconductor master to Github master).
remote: 
remote: For more information, or help resolving this issue, contact
remote: <bioc-devel at r-project.org>. Provide the error, the package name and
remote: any other details we might need.
remote: 
remote: Use
remote: 
remote:     git show ffdb09d480c01535466e89b99e22535672e362a7
remote:     git show 333da75f93af1ca7f5cb9a8443a1d5c963f21280
remote: 
remote: to see body of commits.
remote: 
To git.bioconductor.org:packages/annotatr.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'git at git.bioconductor.org:packages/annotatr.git'
The two commits that are highlighted in the error message are "bump x.y.z versions to odd y after creation of 3_5 branch" commits. I was always confused about the git-svn bridge, but these twin commits are an artifact of that system, I think. The commit that I was trying to push to upstream/master is unrelated to those two commits, and I have committed other items in the new git way prior to the 3.6 release with no issue.

I tried the suggested solution (https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github- <https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github->), but there is a note "This works only if you haven?t pushed the change causing the issue to the Bioconductor repository." I fall into this case.

If anyone has any suggestions for how to deal with this, I would appreciate the help. If more information is required, please say so.

Thanks,
Raymond Cavalcante
Hi Raymond,

I?m trying to figure out why your problem was caused. The duplicates are coming from this commit (ea6c6421b074dbc9411bd6d00547b90bb6168d31), which is a merge. But I?m what I?m trying to figure out is how you?ve been able to push with duplicate commits after that merge.

Please give me sometime.

I will get back to you.

Best,

Nitesh
On Jan 8, 2018, at 2:19 PM, Raymond Cavalcante <rcavalca at umich.edu> wrote:

Hello,

I?m running into the following error when trying to push some changes to annotatr upstream/master:

rcavalca$ git push upstream master
Counting objects: 6, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (6/6), done.
Writing objects: 100% (6/6), 854 bytes | 854.00 KiB/s, done.
Total 6 (delta 5), reused 0 (delta 0)
remote: Error: duplicate commits.
remote: 
remote: There are duplicate commits in your commit history, These cannot be
remote: pushed to the Bioconductor git server. Please make sure that this is
remote: resolved.
remote: 
remote: Take a look at the documentation to fix this,
remote: https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
remote: particularly, point #8 (force Bioconductor master to Github master).
remote: 
remote: For more information, or help resolving this issue, contact
remote: <bioc-devel at r-project.org>. Provide the error, the package name and
remote: any other details we might need.
remote: 
remote: Use
remote: 
remote:     git show ffdb09d480c01535466e89b99e22535672e362a7
remote:     git show 333da75f93af1ca7f5cb9a8443a1d5c963f21280
remote: 
remote: to see body of commits.
remote: 
To git.bioconductor.org:packages/annotatr.git
! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'git at git.bioconductor.org:packages/annotatr.git'

The two commits that are highlighted in the error message are "bump x.y.z versions to odd y after creation of 3_5 branch" commits. I was always confused about the git-svn bridge, but these twin commits are an artifact of that system, I think. The commit that I was trying to push to upstream/master is unrelated to those two commits, and I have committed other items in the new git way prior to the 3.6 release with no issue.

I tried the suggested solution (https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github- <https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github->), but there is a note "This works only if you haven?t pushed the change causing the issue to the Bioconductor repository." I fall into this case.

If anyone has any suggestions for how to deal with this, I would appreciate the help. If more information is required, please say so.

Thanks,
Raymond Cavalcante
	[[alternative HTML version deleted]]

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Hi Raymond,

I have fixed your repository on Bioconductor, and you are able to push changes again. 

Duplicate commits are caused because of ?merge? commits from remotes. Please make sure that before you push from hence forth, or merge, that the duplicate commit issue doesn?t reoccur.

Best,

Nitesh
On Jan 9, 2018, at 1:30 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Raymond,

I?m trying to figure out why your problem was caused. The duplicates are coming from this commit (ea6c6421b074dbc9411bd6d00547b90bb6168d31), which is a merge. But I?m what I?m trying to figure out is how you?ve been able to push with duplicate commits after that merge.

Please give me sometime.

I will get back to you.

Best,

Nitesh 

On Jan 8, 2018, at 2:19 PM, Raymond Cavalcante <rcavalca at umich.edu> wrote:

Hello,

I?m running into the following error when trying to push some changes to annotatr upstream/master:

rcavalca$ git push upstream master
Counting objects: 6, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (6/6), done.
Writing objects: 100% (6/6), 854 bytes | 854.00 KiB/s, done.
Total 6 (delta 5), reused 0 (delta 0)
remote: Error: duplicate commits.
remote: 
remote: There are duplicate commits in your commit history, These cannot be
remote: pushed to the Bioconductor git server. Please make sure that this is
remote: resolved.
remote: 
remote: Take a look at the documentation to fix this,
remote: https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
remote: particularly, point #8 (force Bioconductor master to Github master).
remote: 
remote: For more information, or help resolving this issue, contact
remote: <bioc-devel at r-project.org>. Provide the error, the package name and
remote: any other details we might need.
remote: 
remote: Use
remote: 
remote:     git show ffdb09d480c01535466e89b99e22535672e362a7
remote:     git show 333da75f93af1ca7f5cb9a8443a1d5c963f21280
remote: 
remote: to see body of commits.
remote: 
To git.bioconductor.org:packages/annotatr.git
! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'git at git.bioconductor.org:packages/annotatr.git'

The two commits that are highlighted in the error message are "bump x.y.z versions to odd y after creation of 3_5 branch" commits. I was always confused about the git-svn bridge, but these twin commits are an artifact of that system, I think. The commit that I was trying to push to upstream/master is unrelated to those two commits, and I have committed other items in the new git way prior to the 3.6 release with no issue.

I tried the suggested solution (https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github- <https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github->), but there is a note "This works only if you haven?t pushed the change causing the issue to the Bioconductor repository." I fall into this case.

If anyone has any suggestions for how to deal with this, I would appreciate the help. If more information is required, please say so.

Thanks,
Raymond Cavalcante
	[[alternative HTML version deleted]]

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

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