No such keg: /opt/homebrew/Cellar/r

unknown option ‘--no-build-vignettes --ignore-vignettes --no-manual’

unknown option ‘--no-manual --no-build-vignettes --ignore-vignettes’

'::' or ':::' imports not declared from:

Missing link or links in Rd file 'plot_clusters_used_for_phasing.Rd':

Undocumented code objects:

Undocumented arguments in Rd file 'callHaplotypeSpecificCN.Rd'

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

macOS's Gatekeeper has been disabled for this Cask

pkg-config 0.29.2_3 is already installed and up-to-date. To reinstall 0.29.2_3, run: brew reinstall pkg-config