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