Add `verbose` argument in `check_variables` and `check_ct_data`

[yurovska]

During development of ADaM programs, when not all variables existing in the specs have been derived yet, it is so annoying that check_variables function fails with error and stops execution. Same for ongoing work. Someone adds a new variables to the specs and ADaM program no longer works. What's the point to fail with error just because there is one variable not derived? Shouldn't it be a warning?

Same for check_ct_data. We're far away from eSub and do not want to clean up our specs now by adding all CTs etc. We'll do it when ADaM is final. Until then we'd like to see a warning, not an error.

Our temporary solution is to add the following in .Rprofile:

# Suppress errors in ADaM programs coming from {metatools} functions ----

setHook(
  packageEvent("metatools", "onLoad"),
  function(...) {
    check_variables_original <- metatools::check_variables
    environment(check_variables_original) <- asNamespace("metatools")
    
    assignInNamespace(
      "check_variables",
      function(...) {
        tryCatch(
          check_variables_original(...),
          error = function(e) {
            warning(e$message)
          }
        )
      },
      ns = "metatools"
    )
    
    check_ct_data_original <- metatools::check_ct_data
    environment(check_ct_data_original) <- asNamespace("metatools")
    
    assignInNamespace(
      "check_ct_data",
      function(...) {
        tryCatch(
          check_ct_data_original(...),
          error = function(e) {
            warning(e$message)
          }
        )
      },
      ns = "metatools"
    )
  }
)

[LiamHobby]

@yurovska Thanks for raising this. As of v0.2.0 check_variables has a strict argument which controls whether variables returned after validation are output to the log as errors (strict = TRUE) or as warnings (strict = FALSE).

I agree this should also extend to check_ct_data.

A verbose option is currently being implemented in other functions to give users more control over what they see in the console output. I will look into incorporating this here too.