Clean up build warnings

[mtran-code]

R CMD build and R CMD check and BiocCheck has a ton of warnings/notes. Look into addressing them / trimming them down.

[mtran-code]

00BiocCheck.log

00check.log

[mtran-code]

need to add more runnable examples too, to avoid:

✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.

[mtran-code]

  NB: this package now depends on R (>= 4.1.0)
  WARNING: Added dependency on R >= 4.1.0 because package code uses the
  pipe |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘computeSynergy.R’

Consider refactoring native pipe usage for backwards compatibility?