Thanks Nitesh for your quick reply! > On 13 Feb 2018, at 16:47, Turaga, Nitesh <nitesh.tur...@roswellpark.org> > wrote: > > Hi, > > It seems that there are multiple levels of duplication on your repository. > > You seem to have issued the “merge” with not the current bioconductor devel > but the (now deprecated) GitHub- bioconductor mirror, multiple times. Please > correct me if this is not accurate. I’m wondering why the merge was issued so > many times? >
could be that I pushed several time (wasn't aware of that) - eventually I was just puzzled that it didn't resolve the problem so I tried again... > As far as the fix goes, it would take me a while to track down the “merge” > commits and then “cherry-pick" on to the master branch the commits that are > not duplicated. These seem to be stemming right from the beginning of your > development history. > > The steps you need are: > > 1. Back up master branch (git branch master_backup) > 2. Check merge commit SHA’s (git log --oneline maste) > 3. Reset to commit before the merge, (git reset --hard <commit_SHA>) > 4. Then, overlay commits on top that reset, with latest non-duplicated > commits (git cherry-pick <commit_SHA>) > > You’d have to repeat these steps quite extensively depending on how many > merges you have. > > Take a look at this manual as further help to do this, > http://sethrobertson.github.io/GitFixUm/fixup.html. > > Do these steps on your local repository and push to Github. Once you have > done that, let me know and I’ll take a look at your Github repo, and sync > with Bioconductor if history looks clean. > > If you are unable to fix the repo, then the best way forward it to remove the > pre-receive hook from your repository and deal with the history as is. This > will not effect your package in anyway, just that the git history won’t be > clean. > honestly - I'm afraid my git-knowledge isn't good enough so that I can fix the duplicated commits (I think they still derive from the git git-svn setup). I could live with the git history not being clean. So, from my side, you could go ahead and remove the pre-receive hook. funnily, I have also duplicated commits in ensembldb, but there I'm still able to push to Bioconductor git without problems. best, jo > > Best, > > Nitesh > > >> On Feb 12, 2018, at 5:41 AM, Rainer Johannes <johannes.rai...@eurac.edu> >> wrote: >> >> Dear all, >> >> I'm unable to push my recent changes to FamAgg to the Bioconductor git repo >> (see below for the error message). I did try the suggested fix but without >> any success - seems the duplicated commits are in Bioconductor and not >> github. >> >> thankful for any help or advise >> >> The error message is: >> >> macbookjo:FamAgg jo$ git push origin master >> Everything up-to-date >> macbookjo:FamAgg jo$ git push upstream master >> Counting objects: 13, done. >> Delta compression using up to 8 threads. >> Compressing objects: 100% (13/13), done. >> Writing objects: 100% (13/13), 2.17 KiB | 2.17 MiB/s, done. >> Total 13 (delta 11), reused 0 (delta 0) >> remote: Error: duplicate commits. >> remote: >> remote: There are duplicate commits in your commit history, These cannot be >> remote: pushed to the Bioconductor git server. Please make sure that this is >> remote: resolved. >> remote: >> remote: Take a look at the documentation to fix this, >> remote: >> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/, >> remote: particularly, point #8 (force Bioconductor master to Github master). >> remote: >> remote: For more information, or help resolving this issue, contact >> remote: <bioc-devel@r-project.org>. Provide the error, the package name and >> remote: any other details we might need. >> remote: >> remote: Use >> remote: >> remote: git show 397d05e8ba7d301a9145573210c277f1c6dd66a5 >> remote: git show 6a0c683477b78e231a7eb1b59171baa0bc582ef2 >> remote: >> remote: to see body of commits. >> remote: >> To git.bioconductor.org:packages/FamAgg >> ! [remote rejected] master -> master (pre-receive hook declined) >> error: failed to push some refs to >> 'g...@git.bioconductor.org:packages/FamAgg' >> >> >> macbookjo:FamAgg jo$ git show 397d05e8ba7d301a9145573210c277f1c6dd66a5 >> commit 397d05e8ba7d301a9145573210c277f1c6dd66a5 >> 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/FamAgg@129129 >> bc3139a8-67e5-0310-9ffc-ced21a209358 >> >> diff --git a/DESCRIPTION b/DESCRIPTION >> index c9cb1b7..948b777 100644 >> --- a/DESCRIPTION >> +++ b/DESCRIPTION >> @@ -1,7 +1,7 @@ >> Package: FamAgg >> Type: Package >> Title: Pedigree Analysis and Familial Aggregation >> -Version: 1.4.0 >> +Version: 1.5.0 >> Author: J. Rainer, D. Taliun, C.X. Weichenberger >> Maintainer: Johannes Rainer <johannes.rai...@eurac.edu> >> URL: https://github.com/jotsetung/FamAgg >> >> macbookjo:FamAgg jo$ git show 6a0c683477b78e231a7eb1b59171baa0bc582ef2 >> commit 6a0c683477b78e231a7eb1b59171baa0bc582ef2 >> Author: hpa...@fhcrc.org >> <hpa...@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358> >> 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: >> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FamAgg@129129 >> bc3139a8-67e5-0310-9ffc-ced21a209358 >> >> diff --git a/DESCRIPTION b/DESCRIPTION >> index c9cb1b7..948b777 100644 >> --- a/DESCRIPTION >> +++ b/DESCRIPTION >> @@ -1,7 +1,7 @@ >> Package: FamAgg >> Type: Package >> Title: Pedigree Analysis and Familial Aggregation >> -Version: 1.4.0 >> +Version: 1.5.0 >> Author: J. Rainer, D. Taliun, C.X. Weichenberger >> Maintainer: Johannes Rainer <johannes.rai...@eurac.edu> >> URL: https://github.com/jotsetung/FamAgg >> >> _______________________________________________ >> 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
