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Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, r-lib/actions/setup-pandoc@v1. 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: 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/

replacing previous import 'cli::num_ansi_colors' by 'crayon::num_ansi_colors' when loading 'easypar'

replacing previous import 'cli::num_ansi_colors' by 'crayon::num_ansi_colors' when loading 'easypar'

replacing previous import 'cli::num_ansi_colors' by 'crayon::num_ansi_colors' when loading 'easypar'

replacing previous import 'cli::num_ansi_colors' by 'crayon::num_ansi_colors' when loading 'BMix'

replacing previous import 'crayon::%+%' by 'ggplot2::%+%' when loading 'BMix'

replacing previous import 'cli::num_ansi_colors' by 'crayon::num_ansi_colors' when loading 'BMix'

replacing previous import 'crayon::%+%' by 'ggplot2::%+%' when loading 'BMix'

replacing previous import 'cli::num_ansi_colors' by 'crayon::num_ansi_colors' when loading 'BMix'

replacing previous import 'crayon::%+%' by 'ggplot2::%+%' when loading 'BMix'

plot_SBS.Rd:14: unexpected section header '\value'

plot_SBS.Rd:17: unexpected section header '\description'

plot_SBS.Rd:24: unexpected section header '\examples'

plot_SBS.Rd:33: unexpected END_OF_INPUT '

Found the following significant warnings:

Found the following file with non-ASCII characters:

'::' or ':::' imports not declared from:

prepare_Rd: augment_with_vep.Rd:15-17: Dropping empty section \value

Codoc mismatches from documentation object 'annotate_variants':

Undocumented arguments in documentation object 'as_maftools_obj'

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

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, r-lib/actions/setup-pandoc@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: r-lib/actions/setup-pandoc@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/

plot_SBS.Rd:14: unexpected section header '\value'

plot_SBS.Rd:17: unexpected section header '\description'

plot_SBS.Rd:24: unexpected section header '\examples'

plot_SBS.Rd:33: unexpected END_OF_INPUT '

Found the following significant warnings:

Found the following file with non-ASCII characters:

'::' or ':::' imports not declared from:

prepare_Rd: augment_with_vep.Rd:15-17: Dropping empty section \value

Codoc mismatches from documentation object 'annotate_variants':

Undocumented arguments in documentation object 'as_maftools_obj'

replacing previous import ‘cli::num_ansi_colors’ by ‘crayon::num_ansi_colors’ when loading ‘easypar’

replacing previous import ‘cli::num_ansi_colors’ by ‘crayon::num_ansi_colors’ when loading ‘easypar’

replacing previous import ‘cli::num_ansi_colors’ by ‘crayon::num_ansi_colors’ when loading ‘easypar’

replacing previous import ‘cli::num_ansi_colors’ by ‘crayon::num_ansi_colors’ when loading ‘BMix’

replacing previous import ‘crayon::%+%’ by ‘ggplot2::%+%’ when loading ‘BMix’

replacing previous import ‘cli::num_ansi_colors’ by ‘crayon::num_ansi_colors’ when loading ‘BMix’

replacing previous import ‘crayon::%+%’ by ‘ggplot2::%+%’ when loading ‘BMix’

replacing previous import ‘cli::num_ansi_colors’ by ‘crayon::num_ansi_colors’ when loading ‘BMix’

replacing previous import ‘crayon::%+%’ by ‘ggplot2::%+%’ when loading ‘BMix’

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