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

[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] ‘gWidgets2RGtk2’ is not available in malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64

[Obenchain, Valerie]

It looks like this has cleared up. We couldn't find anything
reproducible so maybe it was a glitch.

Valerie



On 12/13/2016 07:00 AM, Obenchain, Valerie wrote:
> Hi Hemi,
>
> Thanks for the report . We're looking into this ...
>
> Valerie
>
> On 12/11/2016 05:31 PM, Luan Hemi wrote:
>> Dear sir or madam,
>>
>> The gWidgets2RGtk2 seems not to be at malbec1 Linux and causes some
>> problems. Could anyone give some helps?
>>
>> http://bioconductor.org/checkResults/3.4/bioc-LATEST/statTarget/malbec1-buildsrc.html
>>
>>
>>
>> ##
>> ##
>> ###
>> ### Running command:
>> ###
>> ###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs
>> --no-resave-data statTarget
>> ###
>> ##
>> ##
>>
>>
>> * checking for file ‘statTarget/DESCRIPTION’ ... OK
>> * preparing ‘statTarget’:
>> * checking DESCRIPTION meta-information ... OK
>> * installing the package to build vignettes
>>   ---
>> ERROR: dependency ‘gWidgets2RGtk2’ is not available for package ‘statTarget’
>> * removing ‘/tmp/RtmpsXjnzW/Rinst7c64641de7dc/statTarget’
>>   ---
>> ERROR: package installation failed
>>
>> Thanks!
>>
>> Sincerely yours,
>> Hemi
>>
>>  [[alternative HTML version deleted]]
>>
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