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. Martin On 10/1/20, 12:17 PM, "Bioc-devel on behalf of Henrik Bengtsson" <bioc-devel-boun...@r-project.org on behalf of henrik.bengts...@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. /H On Thu, Oct 1, 2020, 09:04 Nitesh Turaga <nturaga.b...@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.bengts...@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.b...@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.mcgr...@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 >> > >> > [[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 >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel