devtools::test() passes, but devtools::check() fails

Question

I am developing a package and all of the 57 tests in the package pass when I use devtools::test(), but there is 1 test that does not pass when I use devtools::check().

-- Failure (test-plot_admissions_discharges_day_of_week.R:53:3): Admission numbers by day of the Week for improvised data --
`result` not equal to `correct_answers`.
Component "Value": Mean absolute difference: 0.7941176

[ FAIL 1 | WARN 4 | SKIP 0 | PASS 56 ]
Error: Test failures
Execution halted

Here is the test file:

test_that("Admission numbers by day of the Week for improvised data", {

  # Specify correct results
  correct_answers <- tibble::tibble(
    Weekday = as.character(c("Mon", "Tue", "Wed", "Thu", "Fri", "Sat", "Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat", "Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat", "Sun")),
    Event = c(
      "Avg_admissions", "Avg_admissions", "Avg_admissions", "Avg_admissions", "Avg_admissions", "Avg_admissions", "Avg_admissions",
      "Avg_discharges", "Avg_discharges", "Avg_discharges", "Avg_discharges", "Avg_discharges", "Avg_discharges", "Avg_discharges",
      "Non_emergency_admissions", "Non_emergency_admissions", "Non_emergency_admissions", "Non_emergency_admissions", "Non_emergency_admissions",
      "Non_emergency_admissions", "Non_emergency_admissions"
    ),
    Value = c(0.0, 0.5, 0.5, 0.5, 0.5, 0.5, 1.0, 2.0, 0.0, 1.5, 1.0, 1.0, 1.0, 1.0, 0.0, 0.5, 0.5, 0.5, 0.5, 0.0, 0.5)
  )

  correct_answers <- correct_answers %>%
    dplyr::arrange(Weekday, Event)

  # Creating input data
  adm <- c("2018-12-09 09:30:00", "2018-12-09 09:30:00", "2018-12-09 09:30:00", "2018-12-11 09:30:00", "2018-12-09 09:30:00", "2018-12-12 09:30:00", "2018-12-09 09:30:00", "2018-12-13 08:00:00", "2018-12-09 09:30:00", "2018-12-14 08:00:00", "2018-12-09 09:30:00", "2018-12-09 09:30:00", "2018-12-15 08:00:00", "2018-12-16 08:00:00", "2018-12-16 08:00:00")
  disch <- c("2018-12-12 09:30:00", "2018-12-10 09:30:00", "2018-12-12 09:30:00", "2018-12-12 09:30:00", "2018-12-13 09:30:00", "2018-12-13 09:30:00", "2018-12-14 08:00:00", "2018-12-14 08:00:00", "2018-12-15 08:00:00", "2018-12-15 08:00:00", "2018-12-16 09:30:00", "2018-12-16 09:30:00", "2018-12-17 08:00:00", "2018-12-17 08:00:00", "2018-12-17 09:00:00")
  spell_class_col <- c(
    "ed_admission", "direct_admission", "ed_admission", "direct_admission", "ed_admission",
    "direct_comp_admission", "ed_admission", "direct_admission", "ed_admission", "direct_admission",
    "ed_admission", "direct_comp_admission", "ed_admission", "ed_admission", "direct_admission"
  )
  spell_start <- as.POSIXct(adm, tz = "Europe/London")
  spell_end <- as.POSIXct(disch, tz = "Europe/London")

  test_avg_adm_disch <- tibble::tibble(
    spell_number = 101:115,
    spell_start,
    spell_end, spell_class_col
  )

  # Run admissions&discharges graph
  result <- plot_admissions_discharges_day_of_week(
    data = test_avg_adm_disch,
    startDate = as.Date("2018-12-10", tz = "Europe/London"),
    endDate = as.Date("2018-12-23", tz = "Europe/London"),
    returnPlot = FALSE,
    hospitalName = "{hospital_name}"
  )

  result$Weekday <- as.character(result$Weekday)

  result <- result %>%
    dplyr::arrange(Weekday, Event)

  # Test results are correct
  expect_equal(tibble::as_tibble(result), tibble::as_tibble(correct_answers), tolerance = 0.01)
})

result and correct_answers are dataframes that are being compared at the end of the test with expect_equal. And they are indeed identical when I execute the code inside test file line by line and call identical() on the dataframes. Value is the column that both dataframes have, and for some reason this is where mismatch happens.

This is what the result and correct_answers dataframes look like when I execute the code manually (as I mentioned previously, they are identical).

As mentioned in Hadley's book, it most likely has something to do with testing environments:

Occasionally you may have a problem where the tests pass when run interactively with devtools::test(), but fail when in R CMD check. This usually indicates that you’ve made a faulty assumption about the testing environment, and it’s often hard to figure it out.

Could someone please help me debug this issue? I checked the following resources but found no luck:

devtools::check() fails where devtools::test() passes because not all test files in testthat are copied over [r]
R CMD check fails, devtools::test() works fine. It talks about the difference in locales that R CMD check and RStudio interactive session uses. I was looking for information how to check the locale of R CMD check but didn't find how.
devtools::test() works but devtools::check() doesn't. Why?
testthat fails within devtools::check but works in devtools::test

Thanks!

I am using R 4.1.0, Windows OS. Here is the DESCRIPTION FILE with the dependencies:

Depends: 
    R (>= 2.10)
Imports: 
    DescTools (>= 0.99.40),
    dplyr (>= 1.0.4),
    forcats (>= 0.5.1),
    ggplot2 (>= 3.3.3),
    ggpubr (>= 0.4.0),
    gtools (>= 3.9.2),
    lazyeval (>= 0.2.2),
    lubridate (>= 1.7.9.2),
    magrittr (>= 2.0.1),
    naniar (>= 0.6.0),
    padr (>= 0.6.0),
    purrr (>= 0.3.4),
    qicharts2 (>= 0.7.1),
    readr (>= 1.4.0),
    reshape2 (>= 1.4.4),
    rlang (>= 0.4.10),
    scales (>= 1.1.1),
    stringr (>= 1.4.0),
    tibble (>= 3.0.6),
    tidyr (>= 1.1.2)
Suggests: 
    knitr (>= 1.31),
    rmarkdown (>= 2.12),
    testthat (>= 3.0.2),
    vdiffr (>= 0.3.3)
VignetteBuilder: 
    knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1

You've not shown us your test code, the code you're trying to test, your input data, your expected output nor the environments in which you're running the tests. It's going to be tricky... — Limey, Jun 07 '22 at 07:40
Hi @Limey, I've added more information to my question. Please let me know if that helps. — Martynas Venckus, Jun 07 '22 at 08:04

devtools::test() passes, but devtools::check() fails

0 Answers0