R CMD check found ERRORs

Process completed with exit code 1.

r-lib/actions/setup-r-dependencies@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/

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/

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 'IgGeneUsage/configure' did not have execute permissions: corrected

There were 2 divergent transitions after warmup. See

Examine the pairs() plot to diagnose sampling problems

Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, r-lib/actions/setup-pandoc@v1, r-lib/actions/setup-r@v1, actions/cache@v2. 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-pandoc@v1, r-lib/actions/setup-r@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/

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

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.