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

Kevin RUE kevinrue67 at gmail.com
Thu Aug 10 16:18:47 CEST 2017

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

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.

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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