[Bioc-devel] Duplicate commit error on and off

Thu Oct 5 19:05:05 CEST 2017

Yes, let's just do it this way.

Thomas

On Thu, Oct 5, 2017 at 9:36 AM Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>
wrote:

> 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 at 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 at 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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> >>>>> _______________________________________________
> >>>>> Bioc-devel at r-project.org mailing list
> >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>
> >>>>
> >>>>
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> >>>
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> >>
> >>
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