[Bioc-devel] git transition for projects with prior git history

Thu Aug 10 20:46:07 CEST 2017

Thanks Nitesh,

I managed to push some changes to my other package "GOexpress" during the
beta a few days ago, so I'm looking forward to the transition next week.
For that package, I didn't hesitate much to clone into a new repository and
start fresh there.

I think I'll do the same for "TVTB", I can always keep the old one for
reference.

Thanks for the reply.
Kevin

On Thu, Aug 10, 2017 at 5:34 PM, Turaga, Nitesh <
Nitesh.Turaga at roswellpark.org> wrote:

> Hi Kevin,
>
> If your Github and SVN repos separated so much, then I’d just wait for the
> transition and then go from there.
>
> Once the git server is alive, you can make a new GitHub repo at that point.
>
> Nitesh
>
>
> > On Aug 10, 2017, at 10:18 AM, Kevin RUE <kevinrue67 at gmail.com> wrote:
> >
> > Hi all,
> >
> > I think I'm facing a similar scenario ("prior history"), although I have
> messed up my original GitHub repo (https://github.com/kevinrue/
> TVTB/commits/master) beyond my ability to synchronise it back to a
> working state.
> >
> > Basically, a few months ago, a bad mix of `git svn rebase` and `git
> merge master` replayed a whole lot of commit, likely the entire local
> history of commits, a couple of times (my Github  master branch now shows
> 1,043 commits, against 333 in the Bioconductor-mirror/TVTB:master. I can
> safely say that I haven't been _that_ productive.
> >
> > After a few attempts to reset/merge/rebase/cry, I gave up the idea of
> reconciliation between my GitHub and the Bioc SVN; I abandoned my own
> GitHub repo and interacted with the SVN directly.
> >
> > Now my GitHub repo is behind the current state of my package in
> git.bioconductor.org (version 1.1.10 vs. 1.3.1), with different commit
> histories, that I can't even start to unravel.
> >
> > At that point, I dream of a way to simply update my own GitHub master to
> the current state of the git.bioconductor.org:packages/TVTB master
> branch, and use that commit as the root of all future development
> (branches). Is that something realistic/worth the effort ?
> >
> > I do have a feeling that the cleanest option would be to abandon my
> GitHub repo, clone from git.bioconductor.org, and make a new GitHub repo
> from that point... but I thought I'd ask one last time before giving up on
> the original repo.
> >
> > Many thanks in advance.
> > Kevin
> >
> >
> >
> >
> > On Fri, Jul 28, 2017 at 7:09 PM, McDavid, Andrew <Andrew_Mcdavid at urmc.
> rochester.edu> wrote:
> > Hi Nitesh,
> >
> > Schematically, my git repo started with commit D, while bioconductor's
> started with A.  It's possible this was because I did something wrong
> managing the bioconductor repo, but since I can't rewrite history, there's
> not anything I can do about that now.  Their "founding" commits are
> distinct.
> >
> >
> >      Bioconductor        A---B---C
> >                                        /     /
> >      Master        D---E---F---G---I
> >
> > Since then, I have I have been cherry-picking changes from master onto
> bioconductor per my understanding of recommended practice.
> > If I try to merge bioconductor onto master, or vice versa, I get the
> unrelated histories warning.  Vlad's suggestion works, but results in
> replaying ~700 commits onto the bioconductor repo...not so nice maybe.
> >
> > The https://github.com/Bioconductor-mirror/MAST.git repo is to make SVN
> commits from the git tree.
> >
> >
> > > On Jul 28, 2017, at 11:33 AM, Turaga, Nitesh
> <Nitesh.Turaga at RoswellPark.org> wrote:
> > >
> > > I would be careful before using the --allow-unrelated-histories flag.
> Please investigate where there is a difference.
> > >
> > > Also, i don't understand why you are using the
> bioconductor-git-mirror? Your non-zero commit history should be related to
> bioconductor git server.
> > >
> > > Best
> > >
> > > Nitesh
> > >
> > > Get Outlook for Android
> > >
> > >
> > >
> > > From: Vladimir Kiselev
> > > Sent: Thursday, July 27, 5:11 PM
> > > Subject: Re: [Bioc-devel] git transition for projects with prior git
> history
> > > To: McDavid, Andrew, bioc-devel at r-project.org
> > >
> > >
> > > Hi Andrew, I solved it by just adding '--allow-unrelated-histories' to
> force the merge: https://stackoverflow.com/questions/37937984/git-
> refusing-to-merge-unrelated-histories Cheers, Vlad On Thu, Jul 27, 2017
> at 9:53 PM McDavid, Andrew < Andrew_Mcdavid at urmc.rochester.edu> wrote: >
> Is there a recommended recipe to utilize the git.bioconductor.org< >
> http://git.bioconductor.org> remote with an existing git repo that has >
> non-zero history? I tried adding the git.bioconductor.org< >
> http://git.bioconductor.org> as a remote, making a branch, and then >
> checking out a branch on that remote, but it gave my computer sad. Do I >
> need to clone a new repo instead? > > Example: > $ git remote -vv > bioc
> https://github.com/Bioconductor-mirror/MAST.git (fetch) > bioc
> https://github.com/Bioconductor-mirror/MAST.git (push) > biocgit
> git at git.bioconductor.org:packages/MAST > (fetch) > biocgit
> git at git.bioconductor.org:packages/MAST > (push) > origin git at github.com:RGLab/MAST.git
> (fetch) > origin git
> >  @github.com:RGLab/MAST.git (push > > $ git fetch biocgit > $ git
> checkout -b bgMaster --track biocgit/master > ... > > ... > $ git merge
> master bgMaster > fatal: refusing to merge unrelated histories > >
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