Yes, let's just do it this way. Thomas
On Thu, Oct 5, 2017 at 9:36 AM Turaga, Nitesh <nitesh.tur...@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 <hpa...@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.gi...@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 <tgi...@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 <hpa...@fredhutch.org> > >> Date: Thu Aug 31 22:28:06 2017 -0700 > >> > >> restore empty folder lost during svn-to-git transition > >> > >> commit 2edc489e4d3ca642a240f062c34528e0d918e11e > >> Author: tgirke <tgi...@citrus.ucr.edu> > >> Date: Wed Aug 23 19:21:04 2017 -0700 > >> > >> moduleload with serveral envir variables > >> > >> commit 1d05c70f27ca083d76bca7ef7be59f43662ba07c > >> Author: tgirke <tgi...@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 <hpa...@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.gi...@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.tur...@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.gi...@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.tur...@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.tur...@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.gi...@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 g...@git.bioconductor.org:packages/systemPipeR.git > >>>>>> ! [rejected] master -> master (non-fast-forward) > >>>>>> error: failed to push some refs to 'g...@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 > >>>>>>> > >>>>> > >>>>> > >>>>> > >>>>> This email message may contain legally privileged and/or > confidential information. 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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. > >>> > >>> > >>> > >>> 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. > >> > >> > >> > >> This email message may contain legally privileged and/or confidential > information. 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