Changes from devtools::check

[pdiakumis]

Keeping these PRs short.

Functions

• Grabbed the source of xfun::strip_html from {xfun} and just copied it into {pcgrr} itself to save from an extra dependency.
• Did the same for MutationalPatterns:::.resample_mut_mat since that's an unexported function from {MutationalPatterns}.
• match_eitems_to_var is commented out in pcgrr/biomarkers.R since it's deprecated. But it's called in get_clin_assocs_snv_indel (also in pcgrr/biomarkers.R) so I've commented that out as well.
• You can refer to {pcgrr} unexported functions without the ::: inside other {pcgrr} code e.g. pcgrr:::load_expression_similarity can simply become load_expression_similarity.
• tibble::has_name can become rlang::has_name and save from requiring the {tibble} dependency.

DESCRIPTION Dependencies

• Removed the following since I couldn't see where they were used in the source code:

  • BiocGenerics
  • caret
  • ggpubr
  • IRanges
  • randomForest
  • usethis (this is only for dev + data-raw)

• Added following:

  • cpsr
  • CNAqc
  • readr
  • stringi

[sigven]

All sensible edits, some old dependencies (IRanges) coming from previous CNA annotation routine. caret and randomForest are also not necessary, msi.R only uses stats::predict on an existing prediction model, I think that should work.