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

2 messages · Joseph Lee Jing Xian, Nitesh Turaga

Joseph Lee Jing Xian
# 
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:
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
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