[Bioc-devel] Initial setup of git svn with existing GitHub repo - upstream working tree history error

2016-12-19 Thread Keegan Korthauer 
Hi bioc-devel,

I am trying set up git svn for my existing GitHub repo for my Bioconductor 
package scDD.  I would like to be able to keep all of the development history 
in my preexisting GitHub repo, so I followed the instructions for Scenario 2 at 
http://bioconductor.org/developers/how-to/git-mirror/ 
.  However, when I try 
the ‘git svn rebase’ command I get the ‘dreaded’ error mentioned in the 
troubleshooting section (‘unable to determine upstream SVN information from 
working tree history’).  

I guessed that this error was a result of some commits that were made between 
the package being accepted to Bioconductor and the current state of my Github 
repo’s master branch.  I followed the directions a the file that was linked to 
as a reference in the troubleshooting section of the above link 
(http://stackoverflow.com/questions/9805980/unable-to-determine-upstream-svn-information-from-working-tree-history
 
),
 including a hard reset of a copy of the master branch to an earlier commit 
that reflects the parent state of the svn repo, then git svn fetch, but I still 
get the same error message as above.  

If anyone has any other suggestions on how I can resolve this conflict between 
svn and git, please let me know.  Thanks!

Best,
Keegan


--
Keegan Korthauer, PhD
Postdoctoral Research Fellow
Department of Biostatistics & Computational Biology, Dana-Farber Cancer 
Institute
Department of Biostatistics, Harvard T. H. Chan School of Public Health
http://bcb.dfci.harvard.edu/~keegan



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Re: [Bioc-devel] Initial setup of git svn with existing GitHub repo - upstream working tree history error

2016-12-20 Thread Lukas Weber 
Hi Keegan,

I'm not sure how much this will help you, but I had some similar issues
recently. I also wanted to keep my pre-existing development history in my
personal GitHub repo, which wasn't straightforward. I ended up solving it
by only using 'git cherry-pick' (instead of 'git merge') to transfer
commits between 'master' and 'devel' branches.

Basically I just 'git cherry-picked' the commits across, one by one. I
think I had the same problem as you, where I had some extra commits in the
'devel' branch. Note that your SHA hashes will be different in each branch,
but this is fine.

I included some more details in an email to this list on November 16;
hopefully this will be useful.

Best regards,
Lukas


Lukas Weber
PhD student
University of Zurich, Switzerland


On Mon, Dec 19, 2016 at 8:44 PM, Keegan Korthauer 
wrote:

> Hi bioc-devel,
>
> I am trying set up git svn for my existing GitHub repo for my Bioconductor
> package scDD.  I would like to be able to keep all of the development
> history in my preexisting GitHub repo, so I followed the instructions for
> Scenario 2 at http://bioconductor.org/developers/how-to/git-mirror/ <
> http://bioconductor.org/developers/how-to/git-mirror/>.  However, when I
> try the ‘git svn rebase’ command I get the ‘dreaded’ error mentioned in the
> troubleshooting section (‘unable to determine upstream SVN information from
> working tree history’).
>
> I guessed that this error was a result of some commits that were made
> between the package being accepted to Bioconductor and the current state of
> my Github repo’s master branch.  I followed the directions a the file that
> was linked to as a reference in the troubleshooting section of the above
> link (http://stackoverflow.com/questions/9805980/unable-to-
> determine-upstream-svn-information-from-working-tree-history <
> http://stackoverflow.com/questions/9805980/unable-to-
> determine-upstream-svn-information-from-working-tree-history>), including
> a hard reset of a copy of the master branch to an earlier commit that
> reflects the parent state of the svn repo, then git svn fetch, but I still
> get the same error message as above.
>
> If anyone has any other suggestions on how I can resolve this conflict
> between svn and git, please let me know.  Thanks!
>
> Best,
> Keegan
>
>
> --
> Keegan Korthauer, PhD
> Postdoctoral Research Fellow
> Department of Biostatistics & Computational Biology, Dana-Farber Cancer
> Institute
> Department of Biostatistics, Harvard T. H. Chan School of Public Health
> http://bcb.dfci.harvard.edu/~keegan
>
>
>
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>
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> Bioc-devel@r-project.org mailing list
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Re: [Bioc-devel] Initial setup of git svn with existing GitHub repo - upstream working tree history error

2016-12-20 Thread Keegan Korthauer 
Thanks, Lukas!  You are correct that the problem was due to some of the commits 
between master and devel and I was able to remedy the issue by 'git 
cherry-pick’ on them one-by-one.  

Best,
Keegan

> On Dec 20, 2016, at 9:57 AM, Lukas Weber  wrote:
> 
> Hi Keegan,
> 
> I'm not sure how much this will help you, but I had some similar issues 
> recently. I also wanted to keep my pre-existing development history in my 
> personal GitHub repo, which wasn't straightforward. I ended up solving it by 
> only using 'git cherry-pick' (instead of 'git merge') to transfer commits 
> between 'master' and 'devel' branches.
> 
> Basically I just 'git cherry-picked' the commits across, one by one. I think 
> I had the same problem as you, where I had some extra commits in the 'devel' 
> branch. Note that your SHA hashes will be different in each branch, but this 
> is fine.
> 
> I included some more details in an email to this list on November 16; 
> hopefully this will be useful.
> 
> Best regards,
> Lukas
> 
> 
> Lukas Weber
> PhD student
> University of Zurich, Switzerland
> 
> 
> On Mon, Dec 19, 2016 at 8:44 PM, Keegan Korthauer  > wrote:
> Hi bioc-devel,
> 
> I am trying set up git svn for my existing GitHub repo for my Bioconductor 
> package scDD.  I would like to be able to keep all of the development history 
> in my preexisting GitHub repo, so I followed the instructions for Scenario 2 
> at http://bioconductor.org/developers/how-to/git-mirror/ 
>  
>  >.  However, when I 
> try the ‘git svn rebase’ command I get the ‘dreaded’ error mentioned in the 
> troubleshooting section (‘unable to determine upstream SVN information from 
> working tree history’).
> 
> I guessed that this error was a result of some commits that were made between 
> the package being accepted to Bioconductor and the current state of my Github 
> repo’s master branch.  I followed the directions a the file that was linked 
> to as a reference in the troubleshooting section of the above link 
> (http://stackoverflow.com/questions/9805980/unable-to-determine-upstream-svn-information-from-working-tree-history
>  
> 
>  
>   
> >),
>  including a hard reset of a copy of the master branch to an earlier commit 
> that reflects the parent state of the svn repo, then git svn fetch, but I 
> still get the same error message as above.
> 
> If anyone has any other suggestions on how I can resolve this conflict 
> between svn and git, please let me know.  Thanks!
> 
> Best,
> Keegan
> 
> 
> --
> Keegan Korthauer, PhD
> Postdoctoral Research Fellow
> Department of Biostatistics & Computational Biology, Dana-Farber Cancer 
> Institute
> Department of Biostatistics, Harvard T. H. Chan School of Public Health
> http://bcb.dfci.harvard.edu/~keegan 
> 
> 
> 
> [[alternative HTML version deleted]]
> 
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> 

--
Keegan Korthauer, PhD
Postdoctoral Research Fellow
Department of Biostatistics & Computational Biology, Dana-Farber Cancer 
Institute
Department of Biostatistics, Harvard T. H. Chan School of Public Health
http://bcb.dfci.harvard.edu/~keegan



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