----- Original Message ----- > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "Luca De Sano" <l.des...@campus.unimib.it> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Friday, March 11, 2016 8:33:58 AM > Subject: Re: [Bioc-devel] Your branch and 'bioc/master' have diverged
> ----- Original Message ----- >> From: "Luca De Sano" <l.des...@campus.unimib.it> >> To: "Dan Tenenbaum" <dtene...@fredhutch.org> >> Cc: "bioc-devel" <bioc-devel@r-project.org> >> Sent: Friday, March 11, 2016 4:20:59 AM >> Subject: Re: [Bioc-devel] Your branch and 'bioc/master' have diverged > >> But, after the what you suggest, git and svn be will synchronized? >> > > You would basically need to cherry pick every time you want to get commits > from > git to svn and vice versa. > A better solution might be to delete your git repository (after updating svn with the latest as described earlier), then re-create your github repository, and keep it in sync with svn using this technique: https://github.com/Bioconductor/BiocGithubHelp/wiki/Managing-your-Bioc-code-on-hedgehog-and-github#appendix-i-a-simpler-way It's also probably best to avoid any non-linear commit history in git. Dan > Dan > > >> >> -- >> Luca De Sano >> Research Associate >> >> Department of Informatics, Systems and Communication >> University of Milan Bicocca >> >> Institute of Biomembranes and Bioenergetics of the Italian National >> Research Council (IBBE-CNR) >> >> email: l.des...@campus.unimib.it >> PEC: luca.des...@pec.it >> >> On 10 March 2016 at 19:47, Dan Tenenbaum <dtene...@fredhutch.org> wrote: >> >>> >>> >>> ----- Original Message ----- >>> > From: "Luca De Sano" <l.des...@campus.unimib.it> >>> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> >>> > Cc: "bioc-devel" <bioc-devel@r-project.org> >>> > Sent: Thursday, March 10, 2016 10:21:38 AM >>> > Subject: Re: [Bioc-devel] Your branch and 'bioc/master' have diverged >>> >>> > On 10 March 2016 at 18:17, Dan Tenenbaum <dtene...@fredhutch.org> wrote: >>> > >>> >> >>> >> >>> >> ----- Original Message ----- >>> >> > From: "Luca De Sano" <l.des...@campus.unimib.it> >>> >> > To: "bioc-devel" <bioc-devel@r-project.org> >>> >> > Sent: Thursday, March 10, 2016 3:22:14 AM >>> >> > Subject: [Bioc-devel] Your branch and 'bioc/master' have diverged >>> >> >>> >> > Hi all, >>> >> > I'm trying to update the devel branch of my package following the >>> >> > instruction found in >>> >> https://bioconductor.org/developers/how-to/git-mirrors/ >>> >> > . >>> >> > >>> >> > The repo of my project is: https://github.com/BIMIB-DISCo/TRONCO >>> >> > >>> >> >>From devel I've first tried to do a git merge master, with no results. >>> >> I've >>> >> > then tried the cherry-pick method and all seemed to work well. >>> However, >>> >> > during the git-svn dcommit, I've obtained a: >>> >> > >>> >> > svn: Commit blocked by pre-commit hook (exit code 1) with output: >>> >> > The y in the x.y.z version number should be even in release >>> >> > in file branches/RELEASE_3_2/madman/Rpacks/VegaMC/DESCRIPTION. >>> >> > See http://bioconductor.org/developers/how-to/version-numbering/ >>> >> > >>> >> >>> >> >>> >> Did you really get this commit error message about trying to commit to >>> the >>> >> devel branch of TRONCO? The message refers to the _release_ branch of >>> >> _VegaMC_. If you did get that error message in response to a commit of >>> >> TRONCO, then something is very wrong with that pre-commit hook. >>> >> >>> > >>> > No. Sorry was just a cut&paste error, I was searching the mailing list >>> for >>> > similar errors ... The message was like: >>> > >>> > svn: Commit blocked by pre-commit hook (exit code 1) with output: >>> > The y in the x.y.z version number should be even in release >>> > in file [some path which I don't remember at the >>> > moment]/madman/Rpacks/TRONCO/DESCRIPTION. >>> > See http://bioconductor.org/developers/how-to/version-numbering/ >>> > >>> > >>> > >>> >> >>> >> >>> >> >>> >> > There has been a problem with a commit (a wrong version update which >>> was >>> >> > rejected from svn). >>> >> > >>> >> > I've fixed this problem on my master removing the wrong commit as >>> >> described >>> >> > here http://www.clock.co.uk/blog/deleting-a-git-commit . I've then >>> >> tried to >>> >> > bring those changes on devel doing this: >>> >> > >>> >> >>> >> Which commit was 'wrong'? >>> >> >>> > >>> > The problem was a wrong version update in a commit made one month ago. >>> This >>> > commit triggered the pre-commit hook and, even If I've fixed it with a >>> new >>> > commit, the problem has remained. So, following the instructions >>> mentioned >>> > above, I've removed the commit from the history tree. >>> > >>> > >>> > >>> >> >>> >> >>> >> > - git reset --hard on devel to the last right commit >>> >> > - git cherry-pick on the others commit from my master branch >>> >> > >>> >> > After the cherry-pick, on git, all worked well. The resul of git log >>> is: >>> >> > >>> >> > dex@darthvader ~/project/TRONCO $ git log --graph --decorate >>> >> > --pretty=oneline --abbrev-commit --all >>> >> > * 2e27604 (HEAD, origin/master, origin/development, origin/HEAD, >>> >> master, >>> >> > development, devel) Merge pull request #47 from >>> BIMIB-DISCo/development >>> >> >|\ >>> >> >| * 340c809 date update >>> >> >|/ >>> >> > * 4700191 dependencies update >>> >> > * 31c2cab regex problems >>> >> > [...] >>> >> > >>> >> > I've then tried to commit to svn, but the git svn dcommit >>> >> --add-author-from >>> >> > now isn't workig... >>> >> > >>> >> > dex@darthvader ~/project/TRONCO $ git svn dcommit --add-author-from >>> >> > Unable to determine upstream SVN information from HEAD history. >>> >> > Perhaps the repository is empty. at /usr/lib/git-core/git-svn line >>> 856. >>> >> > >>> >> > And the result of a git status is: >>> >> > >>> >> > dex@darthvader ~/project/TRONCO $ git status >>> >> > On branch devel >>> >> > Your branch and 'bioc/master' have diverged, >>> >> > and have 615 and 25 different commits each, respectively. >>> >> > (use "git pull" to merge the remote branch into yours) >>> >> > >>> >> > nothing to commit, working directory clean >>> >> > >>> >> > >>> >> > The situation at the moment is: >>> >> > >>> >> > >>> >> > - >>> >> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TRONCO/R/ >>> >> > is a mix of old and new version... I don't know why. Some files are >>> up >>> >> to >>> >> > date with my master and some others no. >>> >> > >>> >> > - My master ( https://github.com/BIMIB-DISCo/TRONCO/tree/master ) >>> is >>> >> up >>> >> > to date and I want to bring this on devel >>> >> > >>> >> > Any idea how to fix this? >>> >> >>> >> >>> >> Basically, cherry-pick any commit that is in master but not devel. Then >>> >> try git-svn dcommit. >>> >> >>> >> Dan >>> >> >>> > >>> > This is not possible because some commits has been applyied not entirely >>> to >>> > devel. In >>> > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TRONCO/ some >>> > files seem to be updated with master and some others no. For example open >>> > as.functions.R and caprese.algorith.R: both have been modified with >>> > >>> https://github.com/BIMIB-DISCo/TRONCO/commit/44e3d7a3f361cbe38227d1c74029afb6e6449e3d >>> > , but only as.functions.R seems to be up to date. >>> > >>> > Can you simply revert everything on svn and on the git mirror to this >>> > commit you made? >>> > >>> https://github.com/BIMIB-DISCo/TRONCO/commit/af70ecaba498642e7e19697c51b856cbe3bba8be >>> > >>> > >>> >>> I can but I am not sure it would solve your problem. >>> >>> Another thing you could do is simply: >>> >>> - check out the package using svn >>> - copy the contents of your git repository over the files >>> in the svn working copy >>> - svn commit the svn working copy. >>> >>> You might still have issues in the future when trying to merge from svn or >>> commit from git. But this would solve your immediate problem. >>> >>> Dan >>> >>> >>> >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> >> >>> >> >>> >> > Many thanks! >>> >> > >>> >> > >>> >> > -- >>> >> > Luca De Sano >>> >> > Research Associate >>> >> > >>> >> > Department of Informatics, Systems and Communication >>> >> > University of Milan Bicocca >>> >> > >>> >> > Institute of Biomembranes and Bioenergetics of the Italian National >>> >> > Research Council (IBBE-CNR) >>> >> > >>> >> > email: l.des...@campus.unimib.it >>> >> > PEC: luca.des...@pec.it >>> >> > >>> >> > [[alternative HTML version deleted]] >>> >> > >>> >> > _______________________________________________ >>> >> > Bioc-devel@r-project.org mailing list >>> >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >>> > >>> > >>> > >>> > -- >>> > Luca De Sano >>> > Research Associate >>> > >>> > Department of Informatics, Systems and Communication >>> > University of Milan Bicocca >>> > >>> > Institute of Biomembranes and Bioenergetics of the Italian National >>> > Research Council (IBBE-CNR) >>> > >>> > email: l.des...@campus.unimib.it >>> > PEC: luca.des...@pec.it > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
