[Bioc-devel] Duplicate commit error on and off

Turaga, Nitesh Nitesh.Turaga at RoswellPark.org
Thu Oct 5 18:19:12 CEST 2017 

It would be easier. I can do it and it would take you back to,

commit c84c7b5fbdf1419af5030b66f8a759d29307f40b (git-svn)
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/systemPipeR@129129 bc3139a8-67e5-0310-9ffc-ced21a209358


Give me a thumbs up and I’ll go ahead. 

> On Oct 5, 2017, at 11:03 AM, Thomas Girke <thomas.girke at ucr.edu> wrote:
> 
> Hi Nitesh,
> 
> If the reset to #c84c7b5f is the best option then let's do this. 
> 
> Just wondering, wouldn't it be much easier to run on your end
> 
> git reset --hard <<Commit_ID_prior_to_problematic_commit>>
> git merge --squash HEAD@{1} 
> 
> This would deduplicate everything without losing any commits.
> 
> Thanks,
> 
> Thomas
> 
> On Thu, Oct 05, 2017 at 10:56:53AM +0000, Turaga, Nitesh wrote:
>> Hi Thomas,
>> 
>> Sorry for the email sent to the wrong place earlier.
>> 
>> One way I can help you is, that I can take you back to the “clean” state on August 16th to commit (c84c7b5fbdf1419af5030b66f8a759d29307f40b).
>> 
>> i.e before the commit 
>> 
>> commit 500a8b924b7c8bfd9b4e960b471e1e000032c06f
>> Merge: e6ff3f8 3cd5aee
>> Author: tgirke <tgirke at citrus.ucr.edu>
>> Date:   Thu Aug 17 18:55:36 2017 -0700
>> 
>>    Fixed conflicts in version change
>> 
>> You would have to manually replay all the commits after that on top of that. By this, I mean, all the commits after 500a8b9, need to be cherry-picked and pushed to the repo. But you need to be careful here, because only “non-merge” commits should be cherry picked. This avoids the duplicates on your contaminated branch to not enter the new clean “master” branch.
>> 
>> Non merge commits, 
>> commit 75bca921c1e2c85e8ab36b5a2d006fb2837c1c50
>> commit 49fa6d434c7bc690223c2b0c88c5353386eb39ba
>> commit c73fb18ad737bea84b5c7bc3967c9bea8bcd4b9c
>> 
>> 
>> After doing that, your last 4 commits will look like this,
>> 
>> 
>> commit 9fc03a5719486e333bc1182b07cd6c5e15e8798d (HEAD -> master)
>> Author: Hervé Pagès <hpages at fredhutch.org>
>> Date:   Thu Aug 31 22:28:06 2017 -0700
>> 
>>    restore empty folder lost during svn-to-git transition
>> 
>> commit 2edc489e4d3ca642a240f062c34528e0d918e11e
>> Author: tgirke <tgirke at citrus.ucr.edu>
>> Date:   Wed Aug 23 19:21:04 2017 -0700
>> 
>>    moduleload with serveral envir variables
>> 
>> commit 1d05c70f27ca083d76bca7ef7be59f43662ba07c
>> Author: tgirke <tgirke at citrus.ucr.edu>
>> Date:   Thu Aug 17 20:29:38 2017 -0700
>> 
>>    Fixed gene set naming problem in GOCluster_Report
>> 
>> commit c84c7b5fbdf1419af5030b66f8a759d29307f40b (git-svn)
>> 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/systemPipeR@129129 bc3139a8-67e5-0310-9ffc-ced21a209358
>> 
>> 
>> This has a couple of consequences,
>> 
>> 1. you need to follow (http://master.bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github- ) to switch you master branch to follow bioconductor exactly. 
>> 
>> 2. you and your collaborators, need to re-clone from your GitHub, and work on the new master branch abandoning the old one.
>> 
>> 3. Make sure that all the file changes you’ve made have been moved over.
>> 
>> Let me know if this works for you, and we can go ahead. Another option is, I can do this for you, with a clean “master” on the Bioconductor repo, and you can follow the “force bioconductor-to-github” manual on your end.
>> 
>> Nitesh 
>> 
>> 
>>> On Oct 4, 2017, at 2:38 PM, Thomas Girke <thomas.girke at ucr.edu> wrote:
>>> 
>>> I didn't commit the duplicate fix with git merge --squash since I wanted to do the branch swap as I did with ChemmineR, but now this is not working anymore or there are other problems?
>>> 
>>> One possible solution could be to allow me a one time push with the -f flag with the deduplicated master branch. According to the instructions here (https://goo.gl/xnr9j8) this should be possible but I think it has been disabled. Some of the Bioc/FAQs related to this topic indicate this too. 
>>> 
>>> Thomas
>>> 
>>> On Wed, Oct 4, 2017 at 11:27 AM Turaga, Nitesh <Nitesh.Turaga at roswellpark.org> wrote:
>>> Thanks, I’ll get back to you. I wasn’t sure because the history on that is not the same. It is a few commits short.
>>> 
>>> 
>>> 
>>>> On Oct 4, 2017, at 2:00 PM, Thomas Girke <thomas.girke at ucr.edu> wrote:
>>>> 
>>>> The gitub repos is here:
>>>> https://github.com/tgirke/systemPipeR
>>>> It is also linked from the Bioc page of the package here: http://bioconductor.org/packages/systemPipeR/
>>>> 
>>>> Thomas
>>>> 
>>>> On Wed, Oct 4, 2017 at 8:11 AM Turaga, Nitesh <Nitesh.Turaga at roswellpark.org> wrote:
>>>> Where is your primary development repo on Github? Please send me link.
>>>> 
>>>> Best,
>>>> 
>>>> Nitesh
>>>> 
>>>>> On Oct 4, 2017, at 10:14 AM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:
>>>>> 
>>>>> 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.
>>>>> 
>>>>> Best,
>>>>> 
>>>>> Nitesh
>>>>> 
>>>>>> 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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>>>> 
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>>> 
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