[Bioc-devel] Package size issue

[Lluís Revilla]

Hi Gabriel,

You can find how to use BFG and other related recommendations at the R
devel book:
https://contributions.bioconductor.org/git-version-control.html?q=BFG#removing-large-files-from-history-with-bfg-repo-cleaner

I hope this helps with this and other questions,

Lluís

On Fri, 29 Mar 2024 at 01:05, Ali Sajid Imami <ali.sajid.imami using gmail.com>
wrote:

> Hi,
> I am not part of the core Bioconductor team, but I have been in this
> situation before. I would suggest you use the BFG Repo Cleaner (
> https://rtyley.github.io/bfg-repo-cleaner/) to remove the errant bam file
> from your repo's history. It's very likely that adding and removing the bam
> file means that that file is still part of the history. That should help
> you cut down on the size.
>
>
> Regards,
> Dr. Ali Sajid Imami
> LinkedIn <https://pk.linkedin.com/pub/ali-sajid-imami/50/956/2a6>
>
>
> On Thu, Mar 28, 2024 at 7:17 PM Gabriel.Villamil using mdc-berlin.de <
> Gabriel.Villamil using mdc-berlin.de> wrote:
>
> > Hi!
> >
> > This is my first message to the mailing list so apologies if I am
> breaking
> > any guidelines.
> >
> > I am submitting a package called Ribostan and the build report gives an
> > error that the package tarball exceeds the size requirement. I am also
> > being warned that individual package files exceed the 5MB size limit.
> >
> > The total size of a fresh clone of my package is 5.9MB, but 3.9MB of that
> > is from the single packfile in .git/objects/pack. As I understand, the
> > packfile contains the history of all files that have ever been in the
> > repository, including files that have been deleted.
> >
> > I am wondering if this packfile is what is inflating my package size in
> > the build and whether there is a solution to reduce its size. In case it
> is
> > relevant: at some point a 1.38MB bam file was committed to the repo as
> toy
> > data for running examples, but has since been deleted. I am also
> wondering
> > why an individual file is reported to be exceeding 5MB when I don’t see
> any
> > such file in my repo.
> >
> > Any advice would be very welcome!
> >
> > Best regards,
> > Gabriel
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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