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

The following actions uses node12 which is deprecated and will be forced to run on node16: r-lib/actions/setup-pandoc@v1, actions/cache@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

The following actions uses Node.js version which is deprecated and will be forced to run on node20: actions/checkout@v3, r-lib/actions/setup-pandoc@v1, actions/cache@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

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

HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK is set: not checking for outdated dependents or dependents with broken linkage!

/private/var/folders/6g/_ypptv3n2fs80_zc0xz8p1d40000gn/T/RtmpJjI7AY/Rbuild1297e7b894a/CNAqc/man/plot_SBS.Rd:14: unexpected section header '\value'

/private/var/folders/6g/_ypptv3n2fs80_zc0xz8p1d40000gn/T/RtmpJjI7AY/Rbuild1297e7b894a/CNAqc/man/plot_SBS.Rd:17: unexpected section header '\description'

/private/var/folders/6g/_ypptv3n2fs80_zc0xz8p1d40000gn/T/RtmpJjI7AY/Rbuild1297e7b894a/CNAqc/man/plot_SBS.Rd:24: unexpected section header '\examples'

/private/var/folders/6g/_ypptv3n2fs80_zc0xz8p1d40000gn/T/RtmpJjI7AY/Rbuild1297e7b894a/CNAqc/man/plot_SBS.Rd:33: unexpected END_OF_INPUT '

Found the following significant warnings:

Found the following file with non-ASCII characters:

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

checkRd: (-1) augment_with_maf.Rd:35: Lost braces in \itemize; meant \describe ?

Codoc mismatches from Rd file 'annotate_variants.Rd':

Undocumented arguments in Rd file 'as_maftools_obj.Rd'

unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/macosx/big-sur-arm64/contrib/4.4:

unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/macosx/big-sur-arm64/contrib/4.4:

unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/macosx/big-sur-arm64/contrib/4.4:

unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/macosx/big-sur-arm64/contrib/4.4:

unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/macosx/big-sur-arm64/contrib/4.4:

r-lib/actions/setup-pandoc@v1 is deprecated. Please update your workflow to use the 'v2' version.