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--- re-building ‘command_line_interface.Rmd’ using rmarkdown

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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.

No files were found with the provided path: /Users/runner/work/categoryCompare2/categoryCompare2/check. No artifacts will be uploaded.

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/

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

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

No files were found with the provided path: check. No artifacts will be uploaded.

macOS's Gatekeeper has been disabled for this Cask

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.

'::' or ':::' import not declared from: 'data.table'

Undocumented arguments in Rd file 'gsea_feature_enrichment.Rd'

'::' or ':::' import not declared from: 'withr'

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/

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

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

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.

No files were found with the provided path: /home/runner/work/categoryCompare2/categoryCompare2/check. No artifacts will be uploaded.

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/

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

No files were found with the provided path: check. No artifacts will be uploaded.

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

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.

'::' or ':::' import not declared from: ‘data.table’

Undocumented arguments in Rd file 'gsea_feature_enrichment.Rd'

'::' or ':::' import not declared from: ‘withr’

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/

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