[Bioc-devel] Your branch and 'bioc/master' have diverged

Fri Mar 11 17:21:24 CET 2016

----- Original Message -----
> From: "Luca De Sano" <l.desano at campus.unimib.it>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "bioc-devel" <bioc-devel at 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?
> 
> 

No.
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.desano at campus.unimib.it
> PEC: luca.desano at pec.it
> 
> On 10 March 2016 at 19:47, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
> 
>>
>>
>> ----- Original Message -----
>> > From: "Luca De Sano" <l.desano at campus.unimib.it>
>> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
>> > Cc: "bioc-devel" <bioc-devel at 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 <dtenenba at fredhutch.org> wrote:
>> >
>> >>
>> >>
>> >> ----- Original Message -----
>> >> > From: "Luca De Sano" <l.desano at campus.unimib.it>
>> >> > To: "bioc-devel" <bioc-devel at 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 at 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 at 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 at 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.desano at campus.unimib.it
>> >> > PEC: luca.desano at pec.it
>> >> >
>> >> >       [[alternative HTML version deleted]]
>> >> >
>> >> > _______________________________________________
>> >> > Bioc-devel at 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.desano at campus.unimib.it
>> > PEC: luca.desano at pec.it