Message-ID: <CE5B4C00-457E-40C7-8D9A-51206B5F3277@gmail.com>
Date: 2020-08-14T11:42:46Z
From: Nitesh Turaga
Subject: [Bioc-devel] Bioconductor Package Submission - Removing git pack objects
In-Reply-To: <HK0PR06MB2707549BC8AF4CAAB41DA95BDA400@HK0PR06MB2707.apcprd06.prod.outlook.com>
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 at 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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