R CMD check found WARNINGs

Process completed with exit code 1.

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, r-lib/actions/setup-r@v1, r-lib/actions/setup-pandoc@v1. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

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

r-lib/actions/setup-r@v1 is deprecated. Please update your workflow to use the 'v2' version. Also look at the examples at https://github.com/r-lib/actions/tree/v2/examples because '@v2' workflows are much simpler than 'v1' workflows.

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:

unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:

unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4:

unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4:

unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4:

Undocumented arguments in Rd file 'fill_in_missing_peaks.Rd'

Undocumented arguments in Rd file 'fill_in_missing_peaks.Rd'