[Bioc-devel] Git pack file greater than 5MB

Nitesh Turaga ntur@g@@b|oc @end|ng |rom gm@||@com
Thu Oct 1 17:15:15 CEST 2020


The BiocCheck will complain on the build system about the > 5MB package size. 

The rewrite of the history with BFG cleaner (https://rtyley.github.io/bfg-repo-cleaner/ <https://rtyley.github.io/bfg-repo-cleaner/>) is not as severe as you think it is to be honest. It is just removing these pack files which don’t have a place in the tree structure. These are more often than not, orphan files.

If you are suspect of this solution, I would suggest you make a backup clone of your repo and try it on that first before you touch the main repo. Check the history (git log) to see if anything important is missing. 

But usually a software package has to be below 5MB. If you have some data in there which is needed for the package, consider Experiment Hub. 



> On Sep 30, 2020, at 12:46 PM, McGrath, Max <MAX.MCGRATH using UCDENVER.EDU> wrote:
> Hi all,
> We have a package that is ready for submission, but when running BiocCheck a warning is generated noting that "The following files are over 5MB in size: '.git/objects/pack/pack-xxx...". I've pruned, repacked, and run git gc which reduced the file size from 5.2 to 5.1MB, but I have been unable to reduce it further.
> I'm reaching out to determine if this is an issue, and if so to ask for recommendations for solving it. Currently, the only solution I've come up with is to rewrite the repository's history using a tool like "git-filter-repo", but this is a more drastic action than I would prefer to take. I would greatly appreciate any advice on the matter.
> Thank you,
> Max McGrath
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