Hi Alan,
Did you manage to solve this?
There seems to be objects in your git repo which are bigger than the size which
is required by Bioconductor for a software package. Please check hidden files
as well.
One test you can do is, to clone your package from github and see how much MB
are downloaded to this new location. This is a good test to check which files
are still larger than the limit.
Best,
Nitesh
On 3/4/21, 11:19 AM, "Bioc-devel on behalf of Murphy, Alan E"
<bioc-devel-boun...@r-project.org on behalf of a.mur...@imperial.ac.uk> wrote:
Hi all,
I am working on the development of
EWCE<https://github.com/NathanSkene/EWCE> for submission to Bioconductor. I
have removed some large objects from the package and moved them to a separate
ExperimentHub package however, after their removal, I got a BiocCheck large
file warning.
To deal with the data stored in git history, I followed the instructions to
use the BFG cleaner with the max size set to 5MB. This appeared to work and
some things were removed but yet I still get the warning below:
$warning[1] "The following files are over 5MB in size:
'.git/objects/pack/pack-366a7ab7a2ba4e656f3a9f3f1408be7ab9f41303.pack'"
If I try to rerun the BFG cleaner I get the following output:
Warning : no large blobs matching criteria found in packfiles - does the
repo need to be packed?
I have tried two different methods to using the BFG cleaner, one from
BFG<https://rtyley.github.io/bfg-repo-cleaner/> themselves and one from
Bioconductor<https://bioconductor.org/developers/how-to/git/remove-large-data/>.
I have also completed all steps in both including the prune step:
git reflog expire --expire=now --all && git gc --prune=now --aggressive
I have even tried reducing the max from 5MB to 1MB but still nothing seems
to be left eve at that size. Does anyone know of another way to sort this issue
or have any clue what I may be doing wrong?
Kind regards,
Alan.
Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London
[[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
