[Bioc-devel] "Error: duplicate commits" when pushing FamAgg to Bioconductor git

Wed Feb 14 08:54:04 CET 2018

Thanks Nitesh for your quick reply!

> On 13 Feb 2018, at 16:47, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:
> 
> Hi,
> 
> It seems that there are multiple levels of duplication on your repository. 
> 
> You seem to have issued the “merge” with not the current bioconductor devel but the (now deprecated) GitHub- bioconductor mirror, multiple times. Please correct me if this is not accurate. I’m wondering why the merge was issued so many times? 
> 

could be that I pushed several time (wasn't aware of that) - eventually I was just puzzled that it didn't resolve the problem so I tried again...

> As far as the fix goes, it would take me a while to track down the “merge” commits and then “cherry-pick" on to the master branch the commits that are not duplicated. These seem to be stemming right from the beginning of your development history. 
> 
> The steps you need are:
> 
> 1. Back up master branch (git branch master_backup)
> 2. Check merge commit SHA’s (git log --oneline maste)
> 3. Reset to commit before the merge, (git reset --hard <commit_SHA>)
> 4. Then, overlay commits on top that reset, with latest non-duplicated commits (git cherry-pick <commit_SHA>)
> 
> You’d have to repeat these steps quite extensively depending on how many merges you have.
> 
> Take a look at this manual as further help to do this, http://sethrobertson.github.io/GitFixUm/fixup.html. 
> 
> Do these steps on your local repository and push to Github. Once you have done that, let me know and I’ll take a look at your Github repo, and sync with Bioconductor if history looks clean.
> 
> If you are unable to fix the repo, then the best way forward it to remove the pre-receive hook from your repository and deal with the history as is. This will not effect your package in anyway, just that the git history won’t be clean. 
> 

honestly - I'm afraid my git-knowledge isn't good enough so that I can fix the duplicated commits (I think they still derive from the git git-svn setup). I could live with the git history not being clean. So, from my side, you could go ahead and remove the pre-receive hook.

funnily, I have also duplicated commits in ensembldb, but there I'm still able to push to Bioconductor git without problems.

best, jo

> 
> Best,
> 
> Nitesh 
> 
> 
>> On Feb 12, 2018, at 5:41 AM, Rainer Johannes <Johannes.Rainer at eurac.edu> wrote:
>> 
>> Dear all,
>> 
>> I'm unable to push my recent changes to FamAgg to the Bioconductor git repo (see below for the error message). I did try the suggested fix but without any success - seems the duplicated commits are in Bioconductor and not github.
>> 
>> thankful for any help or advise
>> 
>> The error message is:
>> 
>> macbookjo:FamAgg jo$ git push origin master
>> Everything up-to-date
>> macbookjo:FamAgg jo$ git push upstream master
>> Counting objects: 13, done.
>> Delta compression using up to 8 threads.
>> Compressing objects: 100% (13/13), done.
>> Writing objects: 100% (13/13), 2.17 KiB | 2.17 MiB/s, done.
>> Total 13 (delta 11), 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 397d05e8ba7d301a9145573210c277f1c6dd66a5
>> remote:     git show 6a0c683477b78e231a7eb1b59171baa0bc582ef2
>> remote: 
>> remote: to see body of commits.
>> remote: 
>> To git.bioconductor.org:packages/FamAgg
>> ! [remote rejected] master -> master (pre-receive hook declined)
>> error: failed to push some refs to 'git at git.bioconductor.org:packages/FamAgg'
>> 
>> 
>> macbookjo:FamAgg jo$ git show 397d05e8ba7d301a9145573210c277f1c6dd66a5
>> commit 397d05e8ba7d301a9145573210c277f1c6dd66a5
>> Author: Herve Pages <hpages at fhcrc.org>
>> Date:   Mon Apr 24 19:50:57 2017 +0000
>> 
>>   bump x.y.z versions to odd y after creation of 3_5 branch
>> 
>>   git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FamAgg@129129 bc3139a8-67e5-0310-9ffc-ced21a209358
>> 
>> diff --git a/DESCRIPTION b/DESCRIPTION
>> index c9cb1b7..948b777 100644
>> --- a/DESCRIPTION
>> +++ b/DESCRIPTION
>> @@ -1,7 +1,7 @@
>> Package: FamAgg
>> Type: Package
>> Title: Pedigree Analysis and Familial Aggregation
>> -Version: 1.4.0
>> +Version: 1.5.0
>> Author: J. Rainer, D. Taliun, C.X. Weichenberger
>> Maintainer: Johannes Rainer <johannes.rainer at eurac.edu>
>> URL: https://github.com/jotsetung/FamAgg
>> 
>> macbookjo:FamAgg jo$ git show 6a0c683477b78e231a7eb1b59171baa0bc582ef2
>> commit 6a0c683477b78e231a7eb1b59171baa0bc582ef2
>> Author: hpages at fhcrc.org <hpages at fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
>> Date:   Mon Apr 24 19:50:57 2017 +0000
>> 
>>   bump x.y.z versions to odd y after creation of 3_5 branch
>> 
>>   git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FamAgg@129129 bc3139a8-67e5-0310-9ffc-ced21a209358
>> 
>> diff --git a/DESCRIPTION b/DESCRIPTION
>> index c9cb1b7..948b777 100644
>> --- a/DESCRIPTION
>> +++ b/DESCRIPTION
>> @@ -1,7 +1,7 @@
>> Package: FamAgg
>> Type: Package
>> Title: Pedigree Analysis and Familial Aggregation
>> -Version: 1.4.0
>> +Version: 1.5.0
>> Author: J. Rainer, D. Taliun, C.X. Weichenberger
>> Maintainer: Johannes Rainer <johannes.rainer at eurac.edu>
>> URL: https://github.com/jotsetung/FamAgg
>> 
>> _______________________________________________
>> 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.