Test Failures Found During R CMD Check

[Andrew-Acker125]

We've been running R CMD check on packages for our package registry manager PRISM (Home | PRISM) and noticed that naniar is failing during tests with 27 failures.

The full error output:

checking tests Running spelling.R
Comparing spelling.Rout to spelling.Rout.save ... OK
Running testthat.R
Running the tests in tests/testthat.R failed.
Last 13 lines of output:
  3.     └─testthat::fail(info = info)
  4.       └─testthat:::check_character(info, allow_null = TRUE)
  5.         └─testthat:::stop_input_type(...)
  6.           └─rlang::abort(message, ..., call = call, arg = arg)

  Snapshots

  To review and process snapshots locally:
  * Locate check directory.
  * Copy 'tests/testthat/_snaps' to local package.
  * Run `testthat::snapshot_accept()` to accept all changes.
  * Run `testthat::snapshot_review()` to review all changes.
  [ FAIL 27 | WARN 0 | SKIP 0 | PASS 615 ]
  Error:
  ! Test failures.
  Execution halted

Investigating the errors, we found three categories of failures:

1. "shade" class lost on grouped data (2 failures)

Here is the failing test:
test-special-missing-values.R:

test_that("special missings class is maintained for grouped and ungrouped data", {
  skip_on_cran()
  skip_on_ci()
  expect_equal(class(aq_grouped_recoded$Ozone_NA),
               class(aq_recoded$Ozone_NA))
  expect_true(is_shade(aq_grouped_recoded$Ozone_NA),
              is_shade(aq_recoded$Ozone_NA))
})

The "shade" class is missing from the grouped data, only "factor" remains:

Expected `class(aq_grouped_recoded$Ozone_NA)` to equal `class(aq_recoded$Ozone_NA)`.
Differences:
`actual`:   "factor"         
`expected`: "shade"  "factor"

and another error here:

Error in `fail(msg, info = info, trace_env = trace_env)`:
`info` must be a character vector or `NULL`, not `TRUE`.

2. Snapshot mismatches:

Here are the failing tests:

test-defunct.R:

df <- tibble::tibble(x = c("A", NA))
test_that("miss_var_prop is defunct", {
  expect_snapshot(error = TRUE, miss_var_prop(df))
})
test_that("complete_var_prop is defunct", {
  expect_snapshot(error = TRUE, complete_var_prop(df))
})
test_that("miss_var_pct is defunct", {
  expect_snapshot(error = TRUE, miss_var_pct(df))
})
test_that("complete_var_pct is defunct", {
  expect_snapshot(error = TRUE, complete_var_pct(df))
})
test_that("miss_case_prop is defunct", {
  expect_snapshot(error = TRUE, miss_case_prop(df))
})
test_that("complete_case_prop is defunct", {
  expect_snapshot(error = TRUE, complete_case_prop(df))
})
test_that("miss_case_pct is defunct", {
  expect_snapshot(error = TRUE, miss_case_pct(df))
})
test_that("complete_case_pct is defunct", {
  expect_snapshot(error = TRUE, complete_case_pct(df))
})
test_that("replace_to_na is defunct", {
  expect_snapshot(error = TRUE, replace_to_na(df))
})

All 9 show the same pattern — the error header now includes the function name. Here is one example:

Expected:

Error:
! 'miss_var_prop' is defunct.
Use 'prop_miss_var' instead.
See help("Defunct")

Actual:

Error in `miss_var_prop()`:
! 'miss_var_prop' is defunct.
Use 'prop_miss_var' instead.
See help("Defunct")

3. Visual snapshot mismatches (16 failures)

16 vdiffr::expect_doppelganger failures across test-gg-miss-case.R (8), test-gg-miss-fct.R (1), test-gg-miss-span.R (2), test-gg-miss-var-plot.R (4), test-gg-miss-which.R (1). These are resolved by downgrading to ggplot2 3.5.2. The expected and actual plots appear visually identical. We've attached a zip of the visual diffs for reference:
naniar.zip

Happy to provide any more details or clarity if needed.

[njtierney]

Thank you for this report! I will respond to this and fix as soon as I have time.