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....@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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
