[Bioc-devel] Duplicate commits in Bioconductor commit history

Turaga, Nitesh Nitesh.Turaga at RoswellPark.org
Wed Jan 17 18:40:48 CET 2018

Hi Laurent,

After checking your package, it’s very hard to get rid of the duplicate commits at this stage of development. I don’t think it should effect the build process of your package. 

The only thing it might effect is, when you look back at a later time to specific commit which is duplicated there might be confusion for developers. Just as a helpful tip, duplicate commits happen when you “merge” different sources. So, be careful while merging in the future from a remote.

I’ve enabled you to push to your repository, so this does not hold up your development. 



> On Jan 16, 2018, at 10:15 AM, Laurent Gatto <lg390 at cam.ac.uk> wrote:
> Dear all,
> There are duplicated commit in the Bioconductor commit history of the
> qcmetrics package, which stop me from pushing additional changes. Here
> is an illustration of the problem:
> $ git clone git at git.bioconductor.org:packages/qcmetrics.git
> Cloning into 'qcmetrics'...
> cd remote: Counting objects: 973, done.
> remote: Compressing objects: 100% (429/429), done.
> remote: Total 973 (delta 614), reused 800 (delta 510)
> Receiving objects: 100% (973/973), 4.73 MiB | 1.82 MiB/s, done.
> Resolving deltas: 100% (614/614), done.
> Checking connectivity... done.
> $ cd qcmetrics
> $ echo >> DESCRIPTION
> $ git commit -am "just a test"                             
> [master 209d6e3] just a test
> 1 file changed, 1 insertion(+)
> $ git push
> Counting objects: 23, done.
> Delta compression using up to 4 threads.
> Compressing objects: 100% (3/3), done.
> Writing objects: 100% (3/3), 280 bytes | 0 bytes/s, done.
> Total 3 (delta 2), 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 fe33ea0a9221f5dbeea0581d1d2381df965d10ce
> remote:     git show 2b089e21267bccbe23416bf756bff01036623aec
> remote: 
> remote: to see body of commits.
> remote: 
> To git at git.bioconductor.org:packages/qcmetrics.git
> ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 'git at git.bioconductor.org:packages/qcmetrics.git'
> If I look at the documentation suggested above, I understand that this
> is relevant for duplicated commits in github and bioconductor
> histories.
> Any idea how to address this within Bioconductor?
> Thank you in advance.
> Laurent
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