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

[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:

> 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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