skip more tests on windows

tests/testthat/test-ael01_nollt.R

@@ -1,7 +1,6 @@
 # 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")
   )
@@ -10,6 +9,7 @@ test_that("ael01_nollt works with admh dataset", {
 
 
 test_that("ael01_nollt works with non-default label", {
+  skip_on_os("windows")
   proc_data <- syn_data
   attr(proc_data$adae$AETERM, "label") <- "Investigator-Specified\n Adverse Event Term"
   res <- expect_silent(
@@ -22,6 +22,7 @@ test_that("ael01_nollt works with non-default label", {
 })
 
 test_that("ael01_nollt can handle all missing values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(
@@ -35,6 +36,7 @@ test_that("ael01_nollt can handle all missing values", {
 })
 
 test_that("ael01_nollt can handle some missing values", {
+  skip_on_os("windows")
   new_aebodsys <- c(NA, "", as.character(syn_data$adae$AEBODSYS[-c(1, 2)]))
   new_aedecod <- c(NA, "", as.character(syn_data$adae$AEDECOD[-c(1, 2)]))
 
@@ -50,6 +52,7 @@ test_that("ael01_nollt can handle some missing values", {
 })
 
 test_that("ael01_nollt listing can be split by an additional variable", {
+  skip_on_os("windows")
   res <- expect_silent(
     run(
       ael01_nollt,

tests/testthat/test-ael02.R

@@ -1,7 +1,6 @@
 # ael02 ----
 
 test_that("ael02 works with adae dataset", {
-  skip_on_os("windows")
   res <- expect_silent(
     run(ael02, syn_data, dataset = "adae")
   )
@@ -11,6 +10,7 @@ test_that("ael02 works with adae dataset", {
 })
 
 test_that("ael02 can handle all missing values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(

tests/testthat/test-ael03.R

@@ -1,7 +1,6 @@
 # ael03 ----
 
 test_that("ael03 works with adae dataset", {
-  skip_on_os("windows")
   res <- expect_silent(
     run(ael03, syn_data, dataset = "adae")
   )
@@ -11,6 +10,7 @@ test_that("ael03 works with adae dataset", {
 })
 
 test_that("ael03 can handle all missing values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(

tests/testthat/test-aet01.R

@@ -38,6 +38,7 @@ test_that("aet01 can use custom anl_vars", {
 })
 
 test_that("aet01 fails on incomplete data input", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(AESER = NULL)

tests/testthat/test-aet01_aesi.R

@@ -1,7 +1,6 @@
 # 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(
@@ -33,12 +32,14 @@ test_that("aet01_aesi can handle some NA values", {
 })
 
 test_that("aet01_aesi works with `ALL` argument", {
+  skip_on_os("windows")
   proc_data <- syn_data
   res <- expect_silent(run(aet01_aesi, proc_data, aesi_vars = c("ALL")))
   expect_snapshot(cat(export_as_txt(res, lpp = 100, cpp = 200)))
 })
 
 test_that("aet01_aesi_check fails on incomplete data input", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(AEOUT = NULL)

tests/testthat/test-aet02.R

@@ -15,6 +15,7 @@ test_that("aet02 fails on incomplete data input", {
 })
 
 test_that("aet02 handle empty data input", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     filter(

tests/testthat/test-aet03.R

@@ -1,5 +1,4 @@
 test_that("aet03 can handle NA values", {
-  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(
@@ -12,6 +11,7 @@ test_that("aet03 can handle NA values", {
 })
 
 test_that("aet03 can handle some NA values", {
+  skip_on_os("windows")
   new_aebodsys <- c(NA, "", as.character(syn_data$adae$AEBODSYS[-c(1, 2)]))
   new_aedecod <- c(NA, "", as.character(syn_data$adae$AEDECOD[-c(1, 2)]))
   new_asev <- c(NA, "", as.character(syn_data$adae$ASEV[-c(1, 2)]))

tests/testthat/test-aet04.R

@@ -8,7 +8,7 @@ test_that("aet04 can handle NA values", {
 
   res1 <- expect_silent(run(aet04, proc_data))
   expect_snapshot(cat(export_as_txt(res1, lpp = 100)))
-
+  skip_on_os("windows")
   grade_groups <- list(
     "Grade 1-2" = c("1", "2"),
     "Grade 3-4" = c("3", "4"),

tests/testthat/test-aet05.R

@@ -8,6 +8,7 @@ test_that("aet05 can handle NA values", {
 })
 
 test_that("aet05 can handle some NA values", {
+  skip_on_os("windows")
   new_paramcd <- c(
     as.character(syn_data$adsaftte$PARAMCD[1:4]), NA, "",
     as.character(syn_data$adsaftte$PARAMCD[-rep(1:6)])

tests/testthat/test-aet05_all.R

@@ -8,6 +8,7 @@ test_that("aet05_all can handle NA values", {
 })
 
 test_that("aet05_all can handle some NA values", {
+  skip_on_os("windows")
   new_paramcd <- c(NA, "", as.character(syn_data$adsaftte$PARAMCD[-c(1, 2)]))
 
   proc_data <- syn_data

tests/testthat/test-aet10.R

@@ -11,6 +11,7 @@ test_that("aet10 can handle NA values", {
 })
 
 test_that("aet10 can handle some NA values", {
+  skip_on_os("windows")
   new_aedecod <- c(NA, "", as.character(syn_data$adae$AEDECOD[-c(1, 2)]))
 
   proc_data <- syn_data

tests/testthat/test-cfbt01.R

@@ -1,6 +1,7 @@
 # cfbt01 functions ----
 
 test_that("cfbt01 functions with default argument value return expected result with test data", {
+  skip_on_os("windows")
   pre_data <- cfbt01_pre(syn_data, dataset = "advs")
   raw_res <- cfbt01_main(pre_data, dataset = "advs")
   res <- cfbt01_post(raw_res)

tests/testthat/test-chevron_tlg-methods.R

@@ -4,12 +4,12 @@ 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)))
 })
 
 test_that("run works as expected for chevron_t object when auto_pre = FALSE", {
+  skip_on_os("windows")
   proc_data <- syn_adv
   proc_data$adsl <- proc_data$adsl %>%
     mutate(DOMAIN = "ADSL")
@@ -18,19 +18,22 @@ test_that("run works as expected for chevron_t object when auto_pre = FALSE", {
 })
 
 test_that("run works as expected with argument printed", {
+  skip_on_os("windows")
   res <- capture_output(tbl <- run(aet02, syn_adv, prune_0 = TRUE, verbose = TRUE))
   expect_snapshot(cat(res))
   expect_snapshot(cat(export_as_txt(tbl, lpp = 100)))
 })
 
 test_that("run works as expected with argument printed if the user argument is complicated", {
+  skip_on_os("windows")
   user_args <- list(prune_0 = TRUE, not_used = iris, lbl_overall = "All Patients", row_split_var = "AEHLT")
   res <- capture_output(tbl <- run(aet02, syn_adv, user_args = user_args, verbose = TRUE))
   expect_snapshot(cat(res))
   expect_snapshot(cat(export_as_txt(tbl, lpp = 100)))
 })
 
 test_that("run uses the argument passed through the ellipsis in priority", {
+  skip_on_os("windows")
   user_args <- list(prune_0 = TRUE, not_used = iris, lbl_overall = "All Patients", row_split_var = "AEHLT")
   res <- capture_output(
     tbl <- run(
@@ -48,12 +51,14 @@ test_that("run uses the argument passed through the ellipsis in priority", {
 })
 
 test_that("run works as expected with partial match argument", {
+  skip_on_os("windows")
   res <- capture_output(tbl <- run(aet02, syn_adv, prune_0 = TRUE, verbose = TRUE, arm_var = "ARM"))
   expect_snapshot(cat(res))
   expect_snapshot(cat(export_as_txt(tbl, lpp = 100)))
 })
 
 test_that("run displays the symbols when available", {
+  skip_on_os("windows")
   user_args <- list(prune_0 = TRUE, not_used = iris, lbl_overall = "All Patients", row_split_var = "AEHLT")
   arm_param <- "ARM"
   res <- capture_output(
@@ -75,12 +80,14 @@ test_that("run displays the symbols when available", {
 # args_ls ----
 
 test_that("args_ls works as expected", {
+  skip_on_os("windows")
   res <- expect_silent(args_ls(aet04))
   expect_list(res, len = 3, names = "named")
   expect_names(names(res), identical.to = c("main", "preprocess", "postprocess"))
 })
 
 test_that("args_ls works as expected when simplify is TRUE", {
+  skip_on_os("windows")
   res <- expect_silent(args_ls(aet04, simplify = TRUE))
   expect_list(res, len = 7, names = "named")
   expect_names(
@@ -92,6 +99,7 @@ test_that("args_ls works as expected when simplify is TRUE", {
 })
 
 test_that("args_ls works as expected with custom chevron_tlg object", {
+  skip_on_os("windows")
   obj <- aet04
   preprocess(obj) <- function(adam_db, arm_var = "overwritten", new_arg = "NEW", ...) {
     adam_db
@@ -111,12 +119,14 @@ test_that("args_ls works as expected with custom chevron_tlg object", {
 # main ----
 
 test_that("main works as expected", {
+  skip_on_os("windows")
   skip_on_covr()
   res <- main(aet04)
   expect_identical(res, aet04_main)
 })
 
 test_that("main setter works as expected", {
+  skip_on_os("windows")
   func <- function(adam_db, ...) {
     build_table(basic_table(), adam_db)
   }
@@ -126,6 +136,7 @@ test_that("main setter works as expected", {
 })
 
 test_that("main setter throw an error as expected", {
+  skip_on_os("windows")
   func <- function(adam_db) {
     build_table(basic_table(), adam_db)
   }
@@ -138,19 +149,22 @@ test_that("main setter throw an error as expected", {
 # preprocess ----
 
 test_that("preprocess works as expected", {
+  skip_on_os("windows")
   skip_on_covr()
   res <- preprocess(aet04)
   expect_identical(res, aet04_pre)
 })
 
 test_that("preprocess setter works as expected", {
+  skip_on_os("windows")
   func <- function(adam_db, ...) adam_db
   obj <- aet04
   preprocess(obj) <- func
   expect_identical(obj@preprocess, func)
 })
 
 test_that("preprocess sends an error as expected", {
+  skip_on_os("windows")
   func <- function(adam_db) adam_db
   obj <- aet04
   expect_error(preprocess(obj) <- func, "Variable 'object@preprocess': Must have formal arguments: ....",
@@ -161,18 +175,21 @@ test_that("preprocess sends an error as expected", {
 # postprocess ----
 
 test_that("postprocess works as expected", {
+  skip_on_os("windows")
   res <- postprocess(aet04)
   expect_identical(res, aet04@postprocess)
 })
 
 test_that("postprocess setter works as expected", {
+  skip_on_os("windows")
   func <- function(tlg, ...) tlg
   obj <- aet04
   postprocess(obj) <- func
   expect_identical(obj@postprocess, func)
 })
 
 test_that("postprocess sends an error as expected", {
+  skip_on_os("windows")
   func <- function(tlg) tlg
   obj <- aet04
   expect_error(postprocess(obj) <- func, "Variable 'object@postprocess': Must have formal arguments: ....",
@@ -183,18 +200,21 @@ test_that("postprocess sends an error as expected", {
 # script_funs ----
 
 test_that("script_funs works as expected in interactive mode", {
+  skip_on_os("windows")
   skip_if(!interactive())
   res <- expect_silent(script_funs(aet04, adam_db = "data", args = "args_ls"))
   expect_snapshot(res)
 })
 
 test_that("script_funs works as expected", {
+  skip_on_os("windows")
   res <- expect_silent(script_funs(aet04, adam_db = "data", args = "args_ls"))
   expect_character(res)
 })
 
 
 test_that("script_funs generates a valid script", {
+  skip_on_os("windows")
   withr::with_tempfile("tmp", fileext = ".R", {
     args_list <- list(
       arm_var = "ARM"
@@ -211,6 +231,7 @@ test_that("script_funs generates a valid script", {
 })
 
 test_that("script_funs works for simple template", {
+  skip_on_os("windows")
   res <- expect_silent(script_funs(chevron_simple(), adam_db = "syn_adv"))
   expect_character(res)
 })

tests/testthat/test-cml02a_gl.R

@@ -6,6 +6,7 @@ test_that("cml02a_gl works with adcm dataset", {
 })
 
 test_that("cml02a_gl works with missing data", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adcm$ATC2 <- NA_character_
   expect_silent(res <- run(cml02a_gl, proc_data))
@@ -15,6 +16,7 @@ test_that("cml02a_gl works with missing data", {
 # cml02a_gl functions ----
 
 test_that("cml02a_gl functions work as expected", {
+  skip_on_os("windows")
   expect_silent(
     res <- cml02a_gl_pre(syn_data) %>%
       cml02a_gl_main()

tests/testthat/test-cmt01a.R

@@ -8,6 +8,7 @@ test_that("cmt01a functions with default argument value return expected result w
 })
 
 test_that("cmt01a functions with custom argument value return expected result with test data", {
+  skip_on_os("windows")
   pre_data <- cmt01a_pre(syn_data)
   raw_res <- cmt01a_main(pre_data, summary_labels = list(
     TOTAL = c(
@@ -22,6 +23,7 @@ test_that("cmt01a functions with custom argument value return expected result wi
 # cmt01a ----
 
 test_that("cmt01a can handle all NA values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adcm <- proc_data$adcm %>%
     mutate(
@@ -34,6 +36,7 @@ test_that("cmt01a can handle all NA values", {
 })
 
 test_that("cmt01a can handle some NA values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adcm$ATC2[1:2] <- NA
   proc_data$adcm$CMDECOD[1:2] <- NA

tests/testthat/test-cmt02_pt.R

@@ -10,6 +10,7 @@ test_that("cmt02_pt can handle all NA values", {
 })
 
 test_that("cmt02_pt can handle some NA values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adcm[1:2, c("CMDECOD")] <- NA