[Bioc-devel] ProteomicsAnnotationHubData duplicated commits

Rainer Johannes Joh@nne@@R@iner @ending from eur@c@edu
Mon Sep 3 15:05:39 CEST 2018

Hi Laurent,

I had the same problem with my ensembldb and FamAgg packages (guess the duplicated commits were introduced by my old git-svn setup). The solution for me was to iteratively do a git rebase (`git rebase -i <sha>` with <sha> of the last commit before any duplicates) removing all duplicated commits, replacing the github master with the thus cleaned local master and then asking Nitesh to replace the BioC master branch with the cleaned github master branch. Was quite some manual work, but now I'm free of any duplicates.

cheers, jo

> On 3 Sep 2018, at 12:58, Laurent Gatto <lg390 using cam.ac.uk> wrote:
> Dear Bioc admins,
> I am trying to push the latest changes from my github master branch to
> Bioconductor's upstreas/master (called devel below), but can't due to
> duplicated commits:
> lg390 using elyacin [12:56:09] [~/dev/ProteomicsAnnotationHubData] [devel]
> -> % git push
> Counting objects: 622, done.
> Delta compression using up to 4 threads.
> Compressing objects: 100% (258/258), done.
> Writing objects: 100% (578/578), 77.71 KiB | 0 bytes/s, done.
> Total 578 (delta 321), reused 546 (delta 296)
> remote: Resolving deltas: 100% (321/321), completed with 21 local objects.
> 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 using r-project.org>. Provide the error, the package name and
> remote: any other details we might need.
> remote:
> remote: Use
> remote:
> remote:     git show f2aaed147a2ad8afe6f218830781ded5c3b01041
> remote:     git show 4ffa7d3512996d63d11f06aa5db5448e2dec65f7
> remote:
> remote: to see body of commits.
> remote:
> To git using git.bioconductor.org:packages/ProteomicsAnnotationHubData.git
> ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 'git using git.bioconductor.org:packages/ProteomicsAnnotationHubData.git'
> Any help in fixing this would be welcome.
> Thank you in advance.
> Laurent
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