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/

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

file=R/check_mhc_class.R,line=14,col=4,[indentation_linter] Indentation should be 6 spaces but is 4 spaces.

file=R/check_mhcnuggets_installation.R,line=19,col=24,[object_usage_linter] no visible global function definition for 'get_default_mhcnuggetsr_folder'

file=R/check_mhcnuggets_installation.R,line=20,col=22,[object_usage_linter] no visible global function definition for 'get_default_orm_folder_name'

file=R/check_mhcnuggets_installation.R,line=23,col=6,[indentation_linter] Indentation should be 4 spaces but is 6 spaces.

file=R/check_mhcnuggets_options.R,line=36,col=24,[object_usage_linter] no visible global function definition for 'get_default_orm_folder_name'

file=R/check_mhcnuggets_options.R,line=40,col=35,[object_usage_linter] no visible global function definition for 'get_trained_mhc_2_haplotypes'

file=R/check_mhcnuggets_options.R,line=50,col=35,[object_usage_linter] no visible global function definition for 'get_trained_mhc_1_haplotypes'

file=R/create_mhcnuggets_options.R,line=27,col=24,[object_usage_linter] no visible global function definition for 'get_default_mhcnuggets_folder'

file=R/create_mhcnuggets_options.R,line=28,col=20,[object_usage_linter] no visible global function definition for 'get_mhcnuggets_url'