Hi, I have recently moved my data to an ExperimentHub package and thus need to clean my statistical package's git history. I followed the guides from both the Bioconductor help page and BFG cleaner pages: https://bioconductor.org/developers/how-to/git/remove-large-data/ https://rtyley.github.io/bfg-repo-cleaner/ These appeared to have worked, I set the limit to 5MB and pushed the changes. Now when I run the clean-up I get the following message: Warning : no large blobs matching criteria found in packfiles - does the repo need to be packed? So it appears nothing remains over the 5MB size but when I locally run BiocCheck() the warning message persists: WARNING: The following files are over 5MB in size: '.git/objects/pack/pack-bb385fcbe4bf53b933abe467a62cd836461ac322.pack' Does anyone have experience dealing with an issue like this? The repository is in the following location if anyone is curious: https://github.com/NathanSkene/EWCE Kind regards, Alan. Alan Murphy Bioinformatician Neurogenomics lab UK Dementia Research Institute Imperial College London
[Bioc-devel] Issue removing large data files from git history
2 messages · Murphy, Alan E, Nitesh Turaga
2 days later
Hi, This means that BFG cleaner didn't get rid of all the files. You can trace back the .pack file to a commit in your git log. You can follow something like this post on github, https://github.com/18F/C2/issues/439 to find which file relates to the .pack file you mention. Best, Nitesh ?On 2/24/21, 12:26 PM, "Bioc-devel on behalf of Murphy, Alan E" <bioc-devel-bounces at r-project.org on behalf of a.murphy at imperial.ac.uk> wrote: Hi, I have recently moved my data to an ExperimentHub package and thus need to clean my statistical package's git history. I followed the guides from both the Bioconductor help page and BFG cleaner pages: https://bioconductor.org/developers/how-to/git/remove-large-data/ https://rtyley.github.io/bfg-repo-cleaner/ These appeared to have worked, I set the limit to 5MB and pushed the changes. Now when I run the clean-up I get the following message: Warning : no large blobs matching criteria found in packfiles - does the repo need to be packed? So it appears nothing remains over the 5MB size but when I locally run BiocCheck() the warning message persists: WARNING: The following files are over 5MB in size: '.git/objects/pack/pack-bb385fcbe4bf53b933abe467a62cd836461ac322.pack' Does anyone have experience dealing with an issue like this? The repository is in the following location if anyone is curious: https://github.com/NathanSkene/EWCE Kind regards, Alan. Alan Murphy Bioinformatician Neurogenomics lab UK Dementia Research Institute Imperial College London _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel