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

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Thu Oct 1 18:32:41 CEST 2020

yes Hervé has made this point too -- mucking with the history of the package, potentially breaking historical checkouts (when large files are deleted from the history, too).

It's relevant because when a package is added to our repository we do a full clone of the master branch; an alternative would be to do a --depth 1 clone of the master branch, but to me this doesn't seem ideal at all -- from the Bioconductor perspective the git.bioconductor.org package is definitive, and all we would have would be 'and then a miracle occurred' for early package development. I'm also nervous about side-effects associated with maintaining the Bioconductor and non-Bioconductor repositories that have different historical starts.

My own feel is that most of these cases are packages that are still 'new' and seldom have clones / forks.

One could take a hybrid approach, where if a maintainer insists on the integrity of their git repository (or even automatically, if they do have large files in their history we automatically change strategy) then we do a --depth 1 clone.


On 10/1/20, 12:17 PM, "Bioc-devel on behalf of Henrik Bengtsson" <bioc-devel-bounces using r-project.org on behalf of henrik.bengtsson using gmail.com> wrote:

    I understood that it's a submission. Just wanted to make sure that it's
    clear there might be side effects, e.g. people clone and collaborate also
    before submitting to Bioc and a rewrite might surprise existing
    collaborators etc.


    On Thu, Oct 1, 2020, 09:04 Nitesh Turaga <nturaga.bioc using gmail.com> wrote:

    > This package isn’t yet a Bioconductor package Henrik. It will break other
    > forks most likely. This package hasn’t been submitted to the Contributions
    > either to be reviewed. So this is the time to break what needs to be broken
    > before it’s submitted to Bioconductor and gets into the Bioconductor git
    > repository.
    > Nitesh
    > On Oct 1, 2020, at 11:57 AM, Henrik Bengtsson <henrik.bengtsson using gmail.com>
    > wrote:
    > Doesn't a git rewrite break all existing clones, forks out there? I'm
    > happy to be corrected, if this is not the case.
    > /Henrik
    > On Thu, Oct 1, 2020, 08:16 Nitesh Turaga <nturaga.bioc using gmail.com> wrote:
    >> Hi,
    >> 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.
    >> Best,
    >> Nitesh
    >> > 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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    >> >
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