[Bioc-devel] Duplicate commit error on and off

Turaga, Nitesh Nitesh.Turaga at RoswellPark.org
Wed Oct 4 16:14:46 CEST 2017

Hi Thomas,

The following issue occurred because there was a commit on Aug 17th with all the duplicates. Unfortunately, your upstream repository has been contaminated with duplicate commits. 

Till I figure out a solution on how to fix this, please hold off any further commits.

I’ll keep you posted. You might have to follow a few special instructions to add any commits you have on your local machine now. 



> On Oct 3, 2017, at 10:08 PM, Thomas Girke <thomas.girke at ucr.edu> wrote:
> Hi Nitesh, 
> Sorry for bothering you again about a similar problem. The master/devel branch of 
> my systemPipeR package also contains upstream duplicates in the Bioc repos. However, I am 
> not able to resolve the problem entirely. When using the 'git merge --squash' approach,
> that worked before, then the duplicates can be removed but this time I am ending up in 
> a trap at the push step:
> git push upstream master
> where I am getting the following error: 
> To git at git.bioconductor.org:packages/systemPipeR.git
> ! [rejected]        master -> master (non-fast-forward)
> error: failed to push some refs to 'git at git.bioconductor.org:packages/systemPipeR.git'
> hint: Updates were rejected because the tip of your current branch is behind
> hint: its remote counterpart. Integrate the remote changes (e.g.
> hint: 'git pull ...') before pushing again.
> hint: See the 'Note about fast-forwards' in 'git push --help' for details.
> The solution to this would normally be to run a `git pull` first but when I do this
> then I am getting all the duplicates back which puts me back where I started.  
> Running a git push with the -f argument also doesn't work since the usage of this option 
> gets rejected by the remote.
> Do you have any suggestions what else I should try?
> Thanks,
> Thomas
> On Tue, Sep 12, 2017 at 02:19:44AM +0000, Thomas Girke wrote:
>> The following allowed me to eliminate the duplicated commits in one step
>> via git merge --squash and then successfully push back to the bioc-git
>> server. After this I was able to switch to the swap branch approach to
>> avoid similar problems in the future.
>> Example here for master branch:
>> git checkout master
>> git pull upstream master # just in case
>> git reset --hard <commit_id> # Reset the current branch to the
>> commit right before dups started
>> git merge --squash HEAD@{1} # Squashes duplicated commits from
>> chosen <commit_id> to HEAD@{1} (state right before previous reset
>> step)
>> git commit -am "some_message" # Commit squashed changes
>> git push upstream master # Push to bioc-git server
>> I am not sure if the above is the best solution but I thought I report it
>> here in case others experience similar problems. BTW: in my case the
>> duplicates were all generated in the upstream merge (step 6) of the
>> instructions here: https://goo.gl/wWVEeT. None of the parent branches (on
>> github or bioc) used in this merge step contained duplicated commits at
>> least as far as I have checked so far. Perhaps some of this relates back to
>> the git svn/rebase steps we used under the old git mirror?
>> Just in case, the following command is very helpful to identify duplicate
>> commits based on patch-id. Commits with identical patch-ids are very likely
>> to have identical content.
>> git rev-list master | xargs -r -L1 git diff-tree -m -p | git
>> patch-id | sort | uniq -w40 -D | cut -c42-80  | xargs -r git log
>> --no-walk --pretty=format:"%h %ad %an (%cn) %s" --date-order
>> --date=iso
>> After duplicated commit pairs have been identified, one can check with diff
>> or vimdiff whether their content is identical:
>> git --no-pager show <commit_id1> > zzz1
>> git --no-pager show <commit_id2> > zzz2
>> vimdiff zzz1 zzz2
>> Thomas

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