Input 'save-always' has been deprecated with message: save-always does not work as intended and will be removed in a future release. A separate `actions/cache/restore` step should be used instead. See https://github.com/actions/cache/tree/main/save#always-save-cache for more details.

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'

Input 'save-always' has been deprecated with message: save-always does not work as intended and will be removed in a future release. A separate `actions/cache/restore` step should be used instead. See https://github.com/actions/cache/tree/main/save#always-save-cache for more details.

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/