[Bioc-devel] [ext] Package size issue

[G@briei@Viii@mii m@iii@g oii mdc-berii@@de]

Thank you very much for the advice! Someone else pointed out that there are two big files in the package tarball (but are not in the repo). They are files that are being generated and saved in the current directory when running examples of some functions. The solution I thought of is to add lines to remove the files at the end of the @example code or to have it that the files are generated in a temp directory instead of root. I hope it works or I will have to think of a more elegant solution.

In any case, I think it is good to run the BFG Repo Cleaner anyway.

Best regards,
Gabriel


On 29. Mar 2024, at 13:31, Lluís Revilla <lluis.revilla using gmail.com<mailto:lluis.revilla using gmail.com>> wrote:

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<mailto: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<mailto:Gabriel.Villamil using mdc-berlin.de> <
Gabriel.Villamil using mdc-berlin.de<mailto: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<mailto:Bioc-devel using r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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