[Bioc-devel] Bioconductor Package Submission - Removing git pack objects

[Nitesh Turaga]

Hi,

Please make sure the bare repository is updated with the “removed” artifacts of the .pack files. From what I understand, the .pack files should also be removed by the BFG cleaner. 

Try and follow this https://stackoverflow.com/questions/11050265/remove-large-pack-file-created-by-git <https://stackoverflow.com/questions/11050265/remove-large-pack-file-created-by-git>. There might a command which “might” help, 

	git for-each-ref --format='delete %(refname)' refs/original | git update-ref —stdin
    git reflog expire --expire=now --all
    git gc --aggressive --prune=now
You seem to be doing everything that we would already recommend a novice user with the same issue. 

Try this and if it doesn’t work, I’ll investigate more.

Best,

Nitesh 


> On Aug 14, 2020, at 5:51 AM, Joseph Lee Jing Xian <joseph.lee using u.nus.edu> wrote:
> 
> To whom it may concern:
> 
> I am Joseph, writing on behalf of the developers of proActiv<https://github.com/GoekeLab/proActiv>, a package used to infer promoter activity from RNA-seq data.
> We are in the process of preparing the package for Biconductor submission. So far, the package has cleared R CMD check with no errors or warnings, and cleared R CMD BiocCheck with no errors. However, we're still getting one warning from R CMD BiocCheck regarding individual file size. In particular, we have a couple of offending files (.bed, .rda), one of them being a git pack object (.pack).
> We have followed the suggested pipeline to remove large files with BFG Repo-cleaner:
> 
>> git clone --mirror https://github.com/GoekeLab/proActiv.git
> 
> 
>> java -jar bfg-1.13.0.jar --strip-blobs-bigger-than 5M --no-blob-protection proActiv.git
> 
>> cd proActiv.git
> 
>> git reflog expire --expire=now --all && git gc --prune=now --aggressive
> 
> This removes the individual files (e.g. .bed, .rda) in commit history that were bigger than the stipulated 5M limit, as expected.
> However, cloning the package locally from the bare repository and running R CMD BiocCheck on it still throws the same warning, but with the git pack object as the only offending file.
> How should one go about dealing with hidden git pack objects so that the Bioconductor checks can be passed successfully?
> 
> Thanks,
> Joseph
> 
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> 
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