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neurogenomics / EpiCompare

Comparison, benchmarking & QC of epigenetic datasets
https://doi.org/doi:10.18129/B9.bioc.EpiCompare
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Pull Bioc `RELEASE_3_16` #122

Closed bschilder closed 1 year ago

bschilder commented 1 year ago

@serachoi1230 now that Bioc 3.16 has been released, can you pull the new upstream RELEASE_3_16 branch and then push it to GitHub as a new branch?

bschilder commented 1 year ago

Reminding @serachoi1230 to address this

serachoi1230 commented 1 year ago

thanks @bschilder ! I'll address this sometime next week as I'll have more time

serachoi1230 commented 1 year ago

@bschilder I tried to do this, but I have some permission issues with my work laptop! I'll have to try again with my personal laptop, which I'll have access to next week :(

serachoi1230 commented 1 year ago

still having issues with the size of example report:

remote: Error: file larger than 5 Mb. remote: remote: File name: 'report/EpiCompare_example.html' remote: File size: 6.2 Mb remote: remote: Please see Biocondcutor guidelines remote: https://bioconductor.org/developers/package-guidelines/ remote: To git.bioconductor.org:packages/EpiCompare.git ! [remote rejected] master -> master (pre-receive hook declined) error: failed to push some refs to 'git.bioconductor.org:packages/EpiCompare.git'

Did we come up with a solution?

bschilder commented 1 year ago

@serachoi1230 @Al-Murphy let's work through this in a zoom call when we discuss the manuscript edits.

Al-Murphy commented 1 year ago

Yeah let's discuss, let me know when!

bschilder commented 1 year ago

report/EpiCompare_example.html

@serachoi1230 Looks like you accidentally added the report folder. This should only be included on GitHub and not be pushed upstream to Bioc. So, within git, removing the report folder from your staged files and then trying to push again should fix this.

Al-Murphy commented 1 year ago

Also add the folder to your .gitignore file so it won't happen again in the future

bschilder commented 1 year ago

Also add the folder to your .gitignore file so it won't happen again in the future

@Al-Murphy Actually, we shouldnt do this because it will omit it from all future pushes to GitHub as well. Unless there's some way to specify .gitignore specific to Bioc. The example report needs to stored on GitHub so it can be rendered in the vignette (see here for full explanation: https://github.com/neurogenomics/EpiCompare/issues/124). Unless we put the report in a separate repo, which im not a fan of since it means not all of EpiCompare's docs are in one place.

bschilder commented 1 year ago 
git rm -r --cache report/
serachoi1230 commented 1 year ago

I should push to RELEASE_3_17 right?

bschilder commented 1 year ago

I should push to RELEASE_3_17 right?

@serachoi1230 that's correct, push to the devel version (3.17). You should only push to the release version (currently 3.16) when there's a major bug fix. But all the changes we're making are enhancements, so just push to dev.