trim tests on windows

tests/testthat/test-ael01_nollt.R

@@ -1,6 +1,7 @@
 # ael01_nollt ----
 
 test_that("ael01_nollt works with admh dataset", {
+  skip_on_os("windows")
   res <- expect_silent(
     run(ael01_nollt, syn_data, dataset = "admh", key_cols = c("MHBODSYS", "MHDECOD"), disp_cols = "MHTERM")
   )
@@ -64,6 +65,7 @@ test_that("ael01_nollt listing can be split by an additional variable", {
 })
 
 test_that("split ael01_nollt listing do not display missing values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$admh <- proc_data$admh[proc_data$admh$SEX == "F", ]
 

tests/testthat/test-ael02.R

@@ -1,6 +1,7 @@
 # ael02 ----
 
 test_that("ael02 works with adae dataset", {
+  skip_on_os("windows")
   res <- expect_silent(
     run(ael02, syn_data, dataset = "adae")
   )
@@ -27,6 +28,7 @@ test_that("ael02 can handle all missing values", {
 
 
 test_that("ael02 functions work as expected", {
+  skip_on_os("windows")
   res <- expect_silent(
     ael02_pre(syn_data) %>%
       ael02_main()

tests/testthat/test-ael03.R

@@ -1,6 +1,7 @@
 # ael03 ----
 
 test_that("ael03 works with adae dataset", {
+  skip_on_os("windows")
   res <- expect_silent(
     run(ael03, syn_data, dataset = "adae")
   )
@@ -27,6 +28,7 @@ test_that("ael03 can handle all missing values", {
 # ael03 functions ----
 
 test_that("ael03 functions work as expected", {
+  skip_on_os("windows")
   res <- expect_silent(
     ael03_pre(syn_data) %>%
       ael03_main()

tests/testthat/test-aet01.R

@@ -15,6 +15,7 @@ test_that("aet01 can handle all NA values", {
 })
 
 test_that("aet01 can handle some NA values", {
+  skip_on_os("windows")
   new_aesdth <- c(NA, "", as.character(syn_data$adae$AESDTH[-c(1, 2)]))
   new_aeser <- c(NA, "", as.character(syn_data$adae$AESER[-c(1, 2)]))
 
@@ -30,6 +31,7 @@ test_that("aet01 can handle some NA values", {
 })
 
 test_that("aet01 can use custom anl_vars", {
+  skip_on_os("windows")
   proc_data <- syn_data
   res <- expect_silent(run(aet01, proc_data, anl_vars = list(safety_var = "FATAL")))
   expect_snapshot(cat(export_as_txt(res, lpp = 100)))
@@ -48,6 +50,7 @@ test_that("aet01 fails on incomplete data input", {
 })
 
 test_that("aet01 can use custom medconcept_var", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae$SMQ01 <- with_label(proc_data$adae$SMQ01NAM != "", "SMQ 01")
   res <- expect_silent(
@@ -66,6 +69,7 @@ test_that("aet01 can use custom medconcept_var", {
 })
 
 test_that("aet01 can conditionally show the number of withdrawal", {
+  skip_on_os("windows")
   expect_silent(res <- run(aet01, syn_data, arm_var = "ARM", show_wd = FALSE))
   expect_snapshot(cat(export_as_txt(res, lpp = 100)))
 })

tests/testthat/test-aet01_aesi.R

@@ -1,6 +1,7 @@
 # aet01_aesi ----
 
 test_that("aet01_aesi can handle all NA values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(
@@ -20,6 +21,7 @@ test_that("aet01_aesi can handle all NA values", {
 })
 
 test_that("aet01_aesi can handle some NA values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(

tests/testthat/test-aet02.R

@@ -25,6 +25,7 @@ test_that("aet02 handle empty data input", {
 })
 
 test_that("aet02 can have different levels of row_split", {
+  skip_on_os("windows")
   res1 <- run(aet02, syn_data, row_split_var = NULL)
   res2 <- run(aet02, syn_data, row_split_var = c("AEBODSYS", "AEDECOD"))
   expect_snapshot(cat(export_as_txt(res1, lpp = 100)))

tests/testthat/test-aet03.R

@@ -1,4 +1,5 @@
 test_that("aet03 can handle NA values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(

tests/testthat/test-aet04.R

@@ -26,6 +26,7 @@ test_that("aet04 can handle NA values", {
 })
 
 test_that("aet04 can handle some NA values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae[1:2, c("AEBODSYS", "AEDECOD")] <- NA
   res1 <- expect_silent(run(aet04, proc_data))

tests/testthat/test-cfbt01.R

@@ -10,6 +10,7 @@ test_that("cfbt01 functions with default argument value return expected result w
 # cfbt01 ----
 
 test_that("cfbt01 can handle n = 0 and outputs NE instead of infs and NAs", {
+  skip_on_os("windows")
   proc_data <- dunlin::log_filter(
     syn_data,
     PARAMCD %in% c("DIABP", "SYSBP"), "advs"

tests/testthat/test-chevron_tlg-methods.R

@@ -4,6 +4,7 @@ syn_adv <- syn_data[c("adsl", "adae")]
 syn_adv$adae <- syn_adv$adae[syn_adv$adae$AEBODSYS %in% c("cl A.1", "cl B.1", "cl B.2"), ]
 
 test_that("run works as expected for chevron_t object", {
+  skip_on_os("windows")
   res <- run(aet04, syn_adv, prune_0 = TRUE)
   expect_snapshot(cat(export_as_txt(res, lpp = 100)))
 })

tests/testthat/test-egt01.R

@@ -1,6 +1,7 @@
 # egt01 functions ----
 
 test_that("egt01 functions with default argument value return expected result with test data", {
+  skip_on_os("windows")
   pre_data <- egt01_pre(syn_data)
   raw_res <- egt01_main(pre_data)
   res <- cfbt01_post(raw_res)

tests/testthat/test-ext01.R

@@ -1,6 +1,7 @@
 # ext01 functions ----
 
 test_that("ext01 functions with default argument value return expected result with test data", {
+  skip_on_os("windows")
   pre_data <- ext01_pre(syn_data)
   raw_res <- ext01_main(pre_data)
   res <- ext01_post(raw_res)
@@ -18,6 +19,7 @@ test_that("ext01 functions with categorical data return expected result with tes
 # ext01 ----
 
 test_that("ext01 works", {
+  skip_on_os("windows")
   proc_data <- syn_data
   res1 <- expect_silent(run(ext01, proc_data))
   expect_snapshot(cat(export_as_txt(res1, lpp = 100)))

tests/testthat/test-fstg01.R

@@ -10,6 +10,7 @@ test_that("fstg01 works as expected", {
 # fstg01 ----
 
 test_that("fstg01 works as expected with custom color set", {
+  skip_on_os("windows")
   proc_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI" & ARM %in% c("A: Drug X", "B: Placebo"), "adrs")
 
   res1 <- expect_silent(run(fstg01, proc_data, response = c("CR", "PR"), dataset = "adrs", col = "gray"))
@@ -20,6 +21,7 @@ test_that("fstg01 works as expected with custom color set", {
 })
 
 test_that("fstg01 works if changes are in subgroups, conf_level, and label_all", {
+  skip_on_os("windows")
   proc_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI" & ARM %in% c("A: Drug X", "B: Placebo"), "adrs")
 
   res1 <- expect_silent(run(fstg01, proc_data, response = c("CR", "PR"), subgroups = NULL, dataset = "adrs"))
@@ -33,6 +35,7 @@ test_that("fstg01 works if changes are in subgroups, conf_level, and label_all",
 })
 
 test_that("fstg01 can handle some NA values in subgroups", {
+  skip_on_os("windows")
   proc_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI" & ARM %in% c("A: Drug X", "B: Placebo"), "adrs")
   proc_data$adrs[1:2, "SEX"] <- NA
   proc_data$adrs[3:4, "AGEGR1"] <- NA

tests/testthat/test-fstg02.R

@@ -10,6 +10,7 @@ test_that("fstg02 works as expected", {
 # fstg02 ----
 
 test_that("fstg02 works as expected with custom color set", {
+  skip_on_os("windows")
   proc_data <- dunlin::log_filter(syn_data, PARAMCD == "OS" & ARM %in% c("A: Drug X", "B: Placebo"), "adtte")
 
   res1 <- expect_silent(run(fstg02, proc_data, dataset = "adtte", col = "gray"))
@@ -20,6 +21,7 @@ test_that("fstg02 works as expected with custom color set", {
 })
 
 test_that("fstg02 works if changes are in subgroups, strata_var, conf_level, and label_all", {
+  skip_on_os("windows")
   proc_data <- dunlin::log_filter(syn_data, PARAMCD == "OS" & ARM %in% c("A: Drug X", "B: Placebo"), "adtte")
 
   res1 <- expect_silent(run(fstg02, proc_data, subgroups = NULL, dataset = "adtte"))
@@ -33,6 +35,7 @@ test_that("fstg02 works if changes are in subgroups, strata_var, conf_level, and
 })
 
 test_that("fstg02 can handle some NA values in subgroups", {
+  skip_on_os("windows")
   proc_data <- dunlin::log_filter(syn_data, PARAMCD == "OS" & ARM %in% c("A: Drug X", "B: Placebo"), "adtte")
   proc_data$adtte[1:2, "SEX"] <- NA
   proc_data$adtte[3:4, "AGEGR1"] <- NA

tests/testthat/test-lbt01.R

@@ -1,6 +1,7 @@
 # lbt01 functions ----
 
 test_that("lbt01 functions with default argument value return expected result with test data", {
+  skip_on_os("windows")
   pre_data <- lbt01_pre(syn_data)
   raw_res <- lbt01_main(pre_data)
   res <- cfbt01_post(raw_res)

tests/testthat/test-lbt14.R

@@ -12,13 +12,15 @@ test_that("lbt14 functions with default argument value return expected result wi
 })
 
 test_that("lbt14 functions with default argument value return expected result with test data when direction = high", {
+  skip_on_os("windows")
   pre_data <- lbt14_pre(syn_lab, direction = "high")
   raw_res <- lbt14_main(pre_data, direction = "high")
   res <- lbt14_post(raw_res, direction = "high")
   expect_snapshot(cat(export_as_txt(res, lpp = 100)))
 })
 
 test_that("lbt14 functions with `gr_missing = excl` return expected result with test data", {
+  skip_on_os("windows")
   pre_data <- lbt14_pre(syn_lab, gr_missing = "excl")
   raw_res <- lbt14_main(pre_data)
   res <- lbt14_post(raw_res)
@@ -34,6 +36,7 @@ test_that("lbt14 functions with `gr_missing = gr_0` return expected result with
 
 # lbt14 ----
 test_that("lbt14 can handle all NA values", {
+  skip_on_os("windows")
   proc_data <- syn_lab
   proc_data$adlb <- proc_data$adlb %>%
     mutate(
@@ -65,6 +68,7 @@ test_that("lbt14 can handle some NA values", {
 })
 
 test_that("lbt14 can accept different gr_missing", {
+  skip_on_os("windows")
   res1 <- run(lbt14, syn_lab, gr_missing = "incl")
   res2 <- run(lbt14, syn_lab, gr_missing = "excl")
   res3 <- run(lbt14, syn_lab, gr_missing = "gr_0")
@@ -97,6 +101,7 @@ test_that("lbt14 can handle all NA values with direction = high", {
 })
 
 test_that("lbt14 can handle some NA values with direction = high", {
+  skip_on_os("windows")
   set.seed(1)
   new_btoxgr <- syn_lab$adlb$BTOXGR
   new_btoxgr[sample(seq_along(new_btoxgr), 20)] <- NA
@@ -116,6 +121,7 @@ test_that("lbt14 can handle some NA values with direction = high", {
 })
 
 test_that("lbt14 can accept different gr_missing with direction = high", {
+  skip_on_os("windows")
   proc_data <- syn_lab
   res1 <- run(lbt14, proc_data, gr_missing = "incl", direction = "high")
   res2 <- run(lbt14, proc_data, gr_missing = "excl", direction = "high")

tests/testthat/test-lbt15.R

@@ -10,6 +10,7 @@ test_that("lbt15 functions with default argument value return expected result wi
 # lbt15 ----
 
 test_that("lbt15 can handle all NA values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adlb <- proc_data$adlb %>%
     mutate(
@@ -32,6 +33,7 @@ test_that("lbt15 can handle missing levels", {
 })
 
 test_that("lbt15 can handle missing levels in baseline", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adlb <- proc_data$adlb %>%
     mutate(

tests/testthat/test-mng01.R

@@ -12,6 +12,7 @@ test_that("mng01 works as expected with default argument values", {
 })
 
 test_that("mng01 works as expected with custom argument values", {
+  skip_on_os("windows")
   withr::with_options(opts_partial_match_old, {
     col <- c(
       "B: Placebo" = "black",
@@ -50,6 +51,7 @@ test_that("mng01 works as expected with custom argument values", {
 # mng01 ----
 
 test_that("mng01 works as expected with custom color set", {
+  skip_on_os("windows")
   withr::with_options(opts_partial_match_old, {
     col <- c(
       "B: Placebo" = "black",
@@ -71,6 +73,7 @@ test_that("mng01 works as expected with custom color set", {
 })
 
 test_that("mng01 works as expected with custom line type set", {
+  skip_on_os("windows")
   withr::with_options(opts_partial_match_old, {
     lty <- c(
       "B: Placebo" = "99",
@@ -103,6 +106,7 @@ test_that("mng01 works with table = NULL", {
 })
 
 test_that("mng01 works with combination of x variables", {
+  skip_on_os("windows")
   withr::with_options(opts_partial_match_old, {
     proc_data <- syn_data
     res <- run(

tests/testthat/test-rspt01.R

@@ -6,6 +6,7 @@ test_that("rspt01 works as expected", {
 })
 
 test_that("rspt01 works as expected for stratified and unstratified analysis", {
+  skip_on_os("windows")
   filter_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI", "adrs")
   res <- expect_silent(run(rspt01, filter_data,
     dataset = "adrs",
@@ -26,6 +27,7 @@ test_that("rspt01 works as expected for stratified and unstratified analysis", {
 })
 
 test_that("rspt01 works as expected for unstratified analysis only", {
+  skip_on_os("windows")
   filter_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI", "adrs")
   res <- expect_silent(run(rspt01, filter_data,
     dataset = "adrs",
@@ -44,6 +46,7 @@ test_that("rspt01 works as expected for unstratified analysis only", {
 })
 
 test_that("rspt01 works as expected for stratified analysis only", {
+  skip_on_os("windows")
   filter_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI", "adrs")
   res <- expect_silent(run(rspt01, filter_data,
     dataset = "adrs",
@@ -84,6 +87,7 @@ test_that("rspt01 works if change reference group", {
 })
 
 test_that("rspt01 works if change statistic methods", {
+  skip_on_os("windows")
   filter_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI", "adrs")
   res <- expect_silent(run(rspt01, filter_data,
     dataset = "adrs",
@@ -113,6 +117,7 @@ test_that("rspt01 works if change statistic methods", {
 
 
 test_that("rspt01 works if change confidence interval", {
+  skip_on_os("windows")
   filter_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI", "adrs")
   res <- expect_silent(run(rspt01, filter_data,
     dataset = "adrs",

tests/testthat/test-vst01.R

@@ -1,7 +1,11 @@
 # vst12 functions ----
 
 test_that("vst01 functions with default argument value return expected result with test data", {
-  pre_data <- vst01_pre(syn_data)
+  proc_data <- dunlin::log_filter(
+    syn_data,
+    PARAMCD %in% c("DIABP", "SYSBP"), "advs"
+  )
+  pre_data <- vst01_pre(proc_data)
   raw_res <- vst01_main(pre_data)
   res <- cfbt01_post(raw_res)
   expect_snapshot(cat(export_as_txt(res, lpp = 200)))
@@ -10,6 +14,11 @@ test_that("vst01 functions with default argument value return expected result wi
 # vst01 ----
 
 test_that("run vst01 works as expected", {
-  res <- expect_silent(run(vst01, syn_data))
+  skip_on_os("windows")
+  proc_data <- dunlin::log_filter(
+    syn_data,
+    PARAMCD %in% c("DIABP", "SYSBP"), "advs"
+  )
+  res <- expect_silent(run(vst01, proc_data))
   expect_snapshot(cat(export_as_txt(res, lpp = 200)))
 })