Missing Function Documentation For A Multiple Functions

[mattssca]

The following functions are currently missing documentation:

• bins_to_bedgraph.R
• cache_output.R
• check_file_details.R
• compare_coding_mutation_pattern.R
• copy_no_clobber.R
• gene_mutation_tally.R
• get_template_wildcards.R
• get_unmatched_normals.R
• grob_wildcards.R
• socketWrite.R
• test_glue.R
• web_add_update_page.R

[Kdreval]

Thanks for tracking these! We would also as part of this would probably want the noRd tags to be removed so each function can generate it's own markdown with documentation and be displayed in the help

[mattssca]

100%

[rdmorin]

Some of these aren't actually GAMBLR functions (e.g. socketWrite) and others probably never belonged in GAMBLR to begin with (e.g. test_glue).

[Kdreval]

Here is the current list returned by check:

❯ checking for missing documentation entries ... WARNING
  Undocumented code objects:
    ‘bins_to_bedgraph’ ‘cache_output’ ‘check_config_value’
    ‘check_file_details’ ‘cnames’ ‘coding_class’ ‘coding_vc’
    ‘colour_aliases’ ‘compare_coding_mutation_pattern’ ‘copy_no_clobber’
    ‘gene_mutation_tally’ ‘get_template_wildcards’
    ‘get_unmatched_normals’ ‘grob_wildcards’ ‘handle_metadata’
    ‘maf_header’ ‘rainfall_conv’ ‘required_cols’ ‘sanity_check_metadata’
    ‘socketWrite’ ‘standardize_chr_prefix’ ‘subset_cnstates’
    ‘trim_scale_expression’ ‘vc_nonSynonymous’
    ‘web_initialize_gambl_site’
  All user-level objects in a package should have documentation entries.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.