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

[Turaga, Nitesh]

The SVN repo is the most current version of your package as far as Bioconductor 
goes. Unfortunately, you have totally unrelated histories by the looks of it. 
(This should show up as an error, when you try to “merge”, i.e `git merge 
upstream/master`)

I would suggest moving forward with the new git repo, after the transition is 
done on August 16th. I would not “delete” the repository you have per say, and 
keep a backup. 

Best,

Nitesh

> On Aug 10, 2017, at 6:30 PM, Stephanie M. Gogarten 
>  wrote:
> 
> I tried following the instructions in scenario 9 after adding a remote:
> $ git remote add upstream https://git.bioconductor.org/packages/GENESIS.git
> $ git fetch --all
> Fetching origin
> Fetching upstream
> warning: no common commits
> 
> When I merge both upstream and origin, I see all my commits in duplicate: one 
> from my original repo, and one from Bioconductor.
> 
> My repo has a rather complicated history: original author forked from the 
> Bioc mirror, I forked from his repo, submitted a pull request, he pushed 
> those changes back to SVN. Later I took over maintenance, set the Bioc mirror 
> as a remote, and pushed my changes directly using git cherry-pick.
> 
> I'm guessing that the only reasonable path forward here is to just delete the 
> current repo and start over after the transition, but I'm wondering if anyone 
> else has seen the "no common commits" message, or has any other ideas.
> 
> thanks,
> Stephanie
> 
> On 7/27/17 1:52 PM, McDavid, Andrew wrote:
>> Is there a recommended recipe to utilize the 
>> git.bioconductor.org remote with an existing 
>> git repo that has non-zero history?  I tried adding the 
>> 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 
>> g...@git.bioconductor.org:packages/MAST 
>> (fetch)
>> biocgit 
>> g...@git.bioconductor.org:packages/MAST 
>> (push)
>> origin g...@github.com:RGLab/MAST.git (fetch)
>> origin g...@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
>>  [[alternative HTML version deleted]]
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
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Re: [Bioc-devel] git transition for projects with prior git history

[Turaga, Nitesh]

The SVN repo is the most current version of your package as far as Bioconductor 
goes. Unfortunately, you have totally unrelated histories by the looks of it. 

I would suggest moving forward with the new git repo, after the transition is 
done on August 16th. I would not “delete” the repository you have per say, and 
keep a backup. 

Best,

Nitesh


> On Aug 10, 2017, at 6:30 PM, Stephanie M. Gogarten 
>  wrote:
> 
> I tried following the instructions in scenario 9 after adding a remote:
> $ git remote add upstream https://git.bioconductor.org/packages/GENESIS.git
> $ git fetch --all
> Fetching origin
> Fetching upstream
> warning: no common commits
> 
> When I merge both upstream and origin, I see all my commits in duplicate: one 
> from my original repo, and one from Bioconductor.
> 
> My repo has a rather complicated history: original author forked from the 
> Bioc mirror, I forked from his repo, submitted a pull request, he pushed 
> those changes back to SVN. Later I took over maintenance, set the Bioc mirror 
> as a remote, and pushed my changes directly using git cherry-pick.
> 
> I'm guessing that the only reasonable path forward here is to just delete the 
> current repo and start over after the transition, but I'm wondering if anyone 
> else has seen the "no common commits" message, or has any other ideas.
> 
> thanks,
> Stephanie
> 
> On 7/27/17 1:52 PM, McDavid, Andrew wrote:
>> Is there a recommended recipe to utilize the 
>> git.bioconductor.org remote with an existing 
>> git repo that has non-zero history?  I tried adding the 
>> 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 
>> g...@git.bioconductor.org:packages/MAST 
>> (fetch)
>> biocgit 
>> g...@git.bioconductor.org:packages/MAST 
>> (push)
>> origin g...@github.com:RGLab/MAST.git (fetch)
>> origin g...@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
>>  [[alternative HTML version deleted]]
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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

[Stephanie M. Gogarten]

I tried following the instructions in scenario 9 after adding a remote:
$ git remote add upstream https://git.bioconductor.org/packages/GENESIS.git
$ git fetch --all
Fetching origin
Fetching upstream
warning: no common commits

When I merge both upstream and origin, I see all my commits in 
duplicate: one from my original repo, and one from Bioconductor.


My repo has a rather complicated history: original author forked from 
the Bioc mirror, I forked from his repo, submitted a pull request, he 
pushed those changes back to SVN. Later I took over maintenance, set the 
Bioc mirror as a remote, and pushed my changes directly using git 
cherry-pick.


I'm guessing that the only reasonable path forward here is to just 
delete the current repo and start over after the transition, but I'm 
wondering if anyone else has seen the "no common commits" message, or 
has any other ideas.


thanks,
Stephanie

On 7/27/17 1:52 PM, McDavid, Andrew wrote:

Is there a recommended recipe to utilize the 
git.bioconductor.org remote with an existing git repo 
that has non-zero history?  I tried adding the 
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 
g...@git.bioconductor.org:packages/MAST 
(fetch)
biocgit 
g...@git.bioconductor.org:packages/MAST (push)
origin g...@github.com:RGLab/MAST.git (fetch)
origin g...@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

[[alternative HTML version deleted]]

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

[Turaga, Nitesh]

Thanks Kevin. This is a good test to see that it works as expected. 

Please note that those changes will not carry forward. 

Nitesh


> On Aug 10, 2017, at 2:46 PM, Kevin RUE <kevinru...@gmail.com> wrote:
> 
> 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.tur...@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 <kevinru...@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_mcda...@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.
> >
> >
> >  BioconductorA---B---C
> >/ /
> >  MasterD---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.tur...@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
> > &g

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

[Kevin RUE]

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.tur...@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 <kevinru...@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@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.
> >
> >
> >  BioconductorA---B---C
> >/ /
> >  MasterD---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.tur...@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@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_mcda...@urmc.rochester.edu> wrote: >
> Is

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

[Turaga, Nitesh]

Hi Andrew,

How important are these “founding” commits? The new git server will also start 
from “A”, as they go off the SVN repo state. 

The recommended practice will change once we move to the git server. I would 
not merge the branches, if they have unrelated histories. If it is possible to 
just go from the new git repo produced after the transition, that would be the 
ideal solution.

Should be easy to port specific commits, on top of the git repo, after August 
16th.

Best,

Nitesh


> On Jul 28, 2017, at 2:09 PM, McDavid, Andrew 
> <andrew_mcda...@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.
> 
> 
> BioconductorA---B---C
>   / /
> MasterD---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.tur...@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@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_mcda...@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 
>> g...@git.bioconductor.org:packages/MAST > (fetch) > biocgit 
>> g...@git.bioconductor.org:packages/MAST > (push) > origin 
>> g...@github.com:RGLab/MAST.git (fetch) > origin 
>> g...@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 > > 
>> [[alternative HTML version deleted]] > > 
>> ___ > Bioc-devel@r-project.org 
>> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- 
>> http://genat.uk [[alternative HTML version deleted]] 
>> ___ Bioc-devel@r-project.org 
>> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel 
>> 
>> 
>> This email message may contain legally privileged and/or confidential 
>> information. If you are not the intended recipient(s), or the employee or 
>> agent responsible for the delivery of this message to the intended 
>> recipient(s), you are hereby notified that any disclosure, copying, 
>> distribution, or use of this email message is prohibited. If you have 
>> received this message in error, please notify the sender immediately by 
>> e-mail and delete this email message from your computer. Thank you.
> 



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

[Turaga, Nitesh]

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 <kevinru...@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_mcda...@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.
> 
> 
>  BioconductorA---B---C
>/ /
>  MasterD---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.tur...@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@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_mcda...@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 
> > g...@git.bioconductor.org:packages/MAST > (fetch) > biocgit 
> > g

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

[Kevin RUE]

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_mcda...@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.
>
>
>  BioconductorA---B---C
>/ /
>  MasterD---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.tur...@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@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_mcda...@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
> g...@git.bioconductor.org:packages/MAST > (fetch) > biocgit
> g...@git.bioconductor.org:packages/MAST > (push) > origin 
> g...@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 > >
> [[alternative HTML version deleted]] > > 
> ___
> > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/
> listinfo/bioc-devel > -- ht

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

[McDavid, Andrew]

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.


 BioconductorA---B---C
   / /
 MasterD---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.tur...@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@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_mcda...@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 
> g...@git.bioconductor.org:packages/MAST > (fetch) > biocgit 
> g...@git.bioconductor.org:packages/MAST > (push) > origin 
> g...@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 > > [[alternative HTML version 
deleted]] > > ___ > 
Bioc-devel@r-project.org mailing list > 
https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- http://genat.uk 
[[alternative HTML version deleted]] 
___ Bioc-devel@r-project.org 
mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel 
> 
> 
> This email message may contain legally privileged and/or confidential 
> information. If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited. If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.

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

[Turaga, Nitesh]

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<https://aka.ms/ghei36>



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@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_mcda...@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 
g...@git.bioconductor.org:packages/MAST > (fetch) > biocgit 
g...@git.bioconductor.org:packages/MAST > (push) > origin 
g...@github.com:RGLab/MAST.git (fetch) > origin git@g
 ithub.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 > > [[alternative HTML version 
deleted]] > > ___ > 
Bioc-devel@r-project.org mailing list > 
https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- http://genat.uk 
[[alternative HTML version deleted]] 
___ Bioc-devel@r-project.org 
mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

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

[Vladimir Kiselev]

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_mcda...@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 
> g...@git.bioconductor.org:packages/MAST
> (fetch)
> biocgit 
> g...@git.bioconductor.org:packages/MAST
> (push)
> origin g...@github.com:RGLab/MAST.git (fetch)
> origin g...@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
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
-- 
http://genat.uk

[[alternative HTML version deleted]]

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

[McDavid, Andrew]

Is there a recommended recipe to utilize the 
git.bioconductor.org remote with an existing git 
repo that has non-zero history?  I tried adding the 
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 
g...@git.bioconductor.org:packages/MAST 
(fetch)
biocgit 
g...@git.bioconductor.org:packages/MAST (push)
origin g...@github.com:RGLab/MAST.git (fetch)
origin g...@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

[[alternative HTML version deleted]]

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