[Bioc-devel] query regarding bfg on bioconductor repository

Turaga, Nitesh Nite@h@Tur@g@ @ending from Ro@wellP@rk@org
Wed Oct 31 20:38:48 CET 2018

Hi Shweta,

Please hold off making anymore commits to restfulSE. I’ve noticed some discrepancies in your package pre-release and post-release. I’ll try to correct it the best I can before letting you know. 

The issues seem to be two-fold, duplicate commits and unusually large file package. Your BFG cleaning as we spoke off line succeeded in making the package size smaller, but it seems to have induced more issues as far as contamination of commit history goes. 

I’ll work on this in the next day or so, and let you know. 

You can then sync a fresh copy of the package on the Bioconductor git server.



> On Oct 30, 2018, at 10:32 AM, Shweta Gopaulakrishnan <reshg using channing.harvard.edu> wrote:
> Hi Nitesh, 
> Hope you are doing good ! I am working with bfg to reduce the size of "restfulSE" package. I am able to do so with the github repository but not with the bioconductor repository. 
> The steps I am following for the bioconductor one is :
> > git clone --mirror git using git.bioconductor.org:packages/restfulSE
> > java -jar bfg.jar --strip-blobs-bigger-than 30M restfulSE.git
> > cd restfulSE.git
> > git reflog expire --expire=now --all && git gc --prune=now --aggressive
> > git push 
> I get an error : fatal: This operation must be run in a work tree 
> Is there any other way to push changes upstream after bfg ? 
> Thank you! 
> -- 
> Shweta Gopaulakrishnan,
> Bioinformatician,
> Channing Division of Network Medicine,
> Brigham and Women's Health Hospital,
> Boston,MA 02115
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