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

[Luca De Sano]

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









>
>
> > 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

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