r-lib/actions/check-r-package@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.

file 'vcfR/cleanup' did not have execute permissions: corrected

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, 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/