Adding skip_on_cran() to all tests

Author: Keith Goldfeld

tests/testthat/test-add_data.R

@@ -1,11 +1,13 @@
 # addCondition ----
 test_that("addCondition throws errors.", {
+  skip_on_cran()
   expect_error(addCondition(), class = "simstudy::missingArgument")
   expect_error(addCondition("a"), class = "simstudy::missingArgument")
   expect_error(addCondition(data.frame(), data.frame(), "a"), class = "simstudy::wrongClass")
 })
 
 test_that("addCondition works.", {
+  skip_on_cran()
   def <- defData(varname = "x", formula = "1;10", dist = "uniformInt")
   defC <- defCondition(condition = "x >= 5", formula = "x + 5", dist = "nonrandom")
   defC <- defCondition(defC, condition = "x < 5", formula = "10", dist = "nonrandom")
@@ -20,12 +22,14 @@ test_that("addCondition works.", {
 
 # addColumns ----
 test_that("addColumns throws errors.", {
+  skip_on_cran()
   expect_error(addColumns(), class = "simstudy::missingArgument")
   expect_error(addColumns("a"), class = "simstudy::missingArgument")
   expect_error(addColumns(data.frame(), data.frame()), class = "simstudy::wrongClass")
 })
 
 test_that("addColumns works.", {
+  skip_on_cran()
   def <- defData(varname = "x", formula = "1;10", dist = "uniformInt")
   dt <- genData(100, def)
   def2 <- defDataAdd(varname = "y", formula = "2.3 * (1/x)", dist = "normal")
@@ -34,6 +38,7 @@ test_that("addColumns works.", {
 })
 
 test_that("defRepeatAdd works", {
+  skip_on_cran()
   expect_silent(
     defRepeatAdd(nVars = 4, prefix = "g", formula = "1/3;1/3;1/3", variance = 0, dist = "categorical")
   )
@@ -47,6 +52,7 @@ test_that("defRepeatAdd works", {
 })
 
 test_that("defRepeatAdd throws errors correctly.", {
+  skip_on_cran()
   expect_error(defRepeatAdd(prefix = "b", formula = 5, variance = 3, dist = "normal"),
     class = "simstudy::missingArgument"
   )
@@ -60,6 +66,7 @@ test_that("defRepeatAdd throws errors correctly.", {
 
 # addMarkov ----
 test_that("addMarkov throws errors.", {
+  skip_on_cran()
   d0 <- defData(varname = "xx", formula = 2)
   d0 <- defData(d0, varname = "xy", formula = 5)
   dd <- genData(n = 10, dt = d0)
@@ -94,6 +101,7 @@ test_that("addMarkov throws errors.", {
 # addSynthetic ----
 
 test_that("addSynthetic throws errors.", {
+  skip_on_cran()
 
   ### Create fake "real" data set
 
@@ -125,6 +133,7 @@ test_that("addSynthetic throws errors.", {
 })
 
 test_that("addSynthetic works.", {
+  skip_on_cran()
 
   ### Create fake 'external' data set 'A'
 

tests/testthat/test-conditions.R

@@ -1,4 +1,5 @@
 test_that("conditions have correct class.", {
+  skip_on_cran()
   expect_error(stop(condition(c("error", "custom_Error"), "This is a custom error")),
     class = c("error", "custom_Error")
   )
@@ -11,6 +12,7 @@ test_that("conditions have correct class.", {
 })
 
 test_that("pluralization works.", {
+  skip_on_cran()
   expect_error(argMissingError("arg1"), "argument is missing",
     class = "simstudy::missingArgument"
   )

tests/testthat/test-glue.R

@@ -1,4 +1,5 @@
 test_that("Blocks are collapsed as expected.", {
+  skip_on_cran()
   nums <- 1:3
   num <- 23
   expect_equal(
@@ -14,6 +15,7 @@ test_that("Blocks are collapsed as expected.", {
 })
 
 test_that("numbers are formated as expected.", {
+  skip_on_cran()
   nums <- c(1.23, 0.556, 1 / 3)
   ints <- c(1, 2, 3)
   expect_equal(glueFmt("{nums:.2f}"), as.character(round(nums, 2)))
@@ -22,6 +24,7 @@ test_that("numbers are formated as expected.", {
 })
 
 test_that("numbers are collapsed and formated correctly.", {
+  skip_on_cran()
   ints <- c(1, 2, 3)
   expect_equal(glueFmtC("{ints:02d}"), "01, 02 and 03")
   expect_equal(glueFmtC("{2:.1f}"), "2.0")

tests/testthat/test-group_data.R

@@ -1,5 +1,6 @@
 # .addStrataCode ----
 test_that("strata codes are added as expected.", {
+  skip_on_cran()
   def <- defData(varname = "male", dist = "binary", formula = .5, id = "cid")
   def <- defData(def, varname = "over65", dist = "binary", formula = "-1.7 + .8*male", link = "logit")
   def <- defData(def, varname = "baseDBP", dist = "normal", formula = 70, variance = 40)
@@ -14,6 +15,7 @@ test_that("strata codes are added as expected.", {
 
 # .stratSamp ----
 test_that("stratified samples are drawn correctly.", {
+  skip_on_cran()
   expect_length(.stratSamp(1, 2), 1)
   expect_length(.stratSamp(2, 4), 2)
   expect_length(.stratSamp(50, 3), 50)

tests/testthat/test-internal_utility.R

@@ -1,5 +1,6 @@
 # .parseDotVars ----
 test_that("dotVars are parsed correctly.", {
+  skip_on_cran()
   extVar1 <- 23
   extVar2 <- 42
   res <- list(..extVar1 = 23, ..extVar2 = 42)
@@ -12,6 +13,7 @@ test_that("dotVars are parsed correctly.", {
 })
 
 test_that("variables from different environments are parsed correctly.", {
+  skip_on_cran()
   extVar3 <- 7
   env1 <- new.env()
   env2 <- new.env(parent = env1)
@@ -27,6 +29,7 @@ test_that("variables from different environments are parsed correctly.", {
 
 # .evalWith ----
 test_that("evalWith throws errors.", {
+  skip_on_cran()
   df <- data.frame()
   ext <- list(formula2parse = 2)
 
@@ -35,6 +38,7 @@ test_that("evalWith throws errors.", {
 })
 
 test_that("evalWith output length is correct.", {
+  skip_on_cran()
   df <- data.frame(a = rep.int(5, 5))
   ext <- list(..ev = 2)
 
@@ -43,6 +47,7 @@ test_that("evalWith output length is correct.", {
 })
 
 test_that("evalWith output is Matrix.", {
+  skip_on_cran()
   df <- data.frame(a = rep.int(5, 5))
   ext <- list(..ev = 2)
 
@@ -74,11 +79,13 @@ test_that("probabilities (matrix) are adjusted as documented.", {
 
 # .getDists ----
 test_that("number of Dists is up to date.", {
+  skip_on_cran()
   expect_length(.getDists(), 16)
 })
 
 # .isFormulaScalar ----
 test_that("isFormularScalar works correctly.", {
+  skip_on_cran()
   expect_true(.isFormulaScalar("5 + 3"))
   expect_true(.isFormulaScalar(5 + 3))
 
@@ -89,6 +96,7 @@ test_that("isFormularScalar works correctly.", {
 
 # .isValidVarName ----
 test_that("var names are validated correctly.", {
+  skip_on_cran()
   validNames <- c("var1", "name", "name2", "var1")
   wrongNames <- c("...", "..1", "..5")
 
@@ -103,6 +111,7 @@ test_that("var names are validated correctly.", {
 
 # .isError ----
 test_that("errors are detected correctly.", {
+  skip_on_cran()
   err <- try(nonVar + 4, silent = TRUE)
   noErr <- try(3 + 5, silent = TRUE)
 
@@ -114,6 +123,7 @@ test_that("errors are detected correctly.", {
 
 # .hasValue ----
 test_that("hasValue works.", {
+  skip_on_cran()
   expect_true(.hasValue("value"))
   expect_true((function(x) .hasValue(x))(5))
   expect_true((function(x) .hasValue(x))(NA))
@@ -125,6 +135,7 @@ test_that("hasValue works.", {
 
 # .log2Prob ----
 test_that("log odds are converted correctly.", {
+  skip_on_cran()
   prob <- 0.2
   logOdds <- log(0.25)
 

tests/testthat/test-survival.R

@@ -1,8 +1,10 @@
 test_that("defSurv kicks out transition error", {
+  skip_on_cran()
   expect_error(defSurv(varname = "censor", formula = "-7", shape = 0.55, transition = 150))
 })
 
 test_that("genSurv runs OK", {
+  skip_on_cran()
   dS <- defSurv(varname = "event_1", formula = "-10", shape = 0.3)
   dS <- defSurv(dS, "event_2", "-6.5", shape = 0.4)
   dS <- defSurv(dS, "event_3", "-7", shape = 0.5)
@@ -28,6 +30,7 @@ test_that("genSurv runs OK", {
 })
 
 test_that("genSurv throws errors", {
+  skip_on_cran()
   dS <- defSurv(varname = "event_1", formula = "-10", shape = 0.3)
   dS <- defSurv(dS, "event_2", "-6.5", shape = 0.4)
   dS <- defSurv(dS, "event_3", "-7", shape = 0.5)
@@ -38,6 +41,7 @@ test_that("genSurv throws errors", {
 })
 
 test_that("addCmpRisk works", {
+  skip_on_cran()
   dS <- defSurv(varname = "event_1", formula = "-10", shape = 0.3)
   dS <- defSurv(dS, "event_2", "-6.5", shape = 0.4)
 

tests/testthat/test-utility.R

@@ -44,6 +44,7 @@ test_that("probabilities (vector) are adjusted as documented.", {
 })
 
 test_that("genCatFormula throws errors.", {
+  skip_on_cran()
   expect_error(genCatFormula(), "Need to specify")
   expect_error(genCatFormula(1, 2, 3, n = 5), "or n, not both")
   expect_error(genCatFormula(1.1), "must be less than 1")
@@ -53,16 +54,19 @@ test_that("genCatFormula throws errors.", {
 
 # betaGetShapes ----
 test_that("betaGetShapes throws errors.", {
+  skip_on_cran()
   expect_error(betaGetShapes(1, 12), class = "simstudy::valueError")
   expect_error(betaGetShapes(.5, -5), class = "simstudy::valueError")
 })
 
 test_that("betaGetShapes works.", {
+  skip_on_cran()
   expect_equal(betaGetShapes(.4, 5), list(shape1 = .4 * 5, shape2 = (1 - .4) * 5))
 })
 
 # genMixFormula ----
 test_that("genMixFormula throws errors.", {
+  skip_on_cran()
   expect_error(genMixFormula(), class = "simstudy::missingArgument")
   expect_error(genMixFormula("a", varLength = 3), class = "simstudy::valueError")
   expect_error(genMixFormula("..a", varLength = "b"), class = "simstudy::wrongType")
@@ -72,6 +76,7 @@ test_that("genMixFormula throws errors.", {
 })
 
 test_that("genMixFormula works.", {
+  skip_on_cran()
   expect_equal(genMixFormula("a"), "a | 1")
   expect_equal(genMixFormula(c("a", "..b"), c(.3, .7)), "a | 0.3 + ..b | 0.7")
   expect_equal(
@@ -83,6 +88,7 @@ test_that("genMixFormula works.", {
 # survGetParams ----
 
 test_that("survGetParams throws errors.", {
+  skip_on_cran()
   expect_error(survGetParams(), class = "simstudy::missingArgument")
   expect_error(survGetParams(c(100, .5)), class = "simstudy::wrongClass")
   points <- list(c(280, 0.85), c(165, .45))
@@ -96,6 +102,7 @@ test_that("survGetParams throws errors.", {
 })
 
 test_that("survGetParam works.", {
+  skip_on_cran()
   points <- list(c(50, 0.90), c(100, 0.10))
   expect_equal(survGetParams(points), c(-19.658, 0.225), tolerance = .001)
   points <- list(c(60, 0.90), c(100, .75), c(200, .25), c(250, .10))
@@ -105,12 +112,14 @@ test_that("survGetParam works.", {
 # plotSurv ----
 
 test_that("survParamPlot throws errors.", {
+  skip_on_cran()
   expect_error(survParamPlot(), class = "simstudy::missingArgument")
   expect_error(survParamPlot(formula = -10), class = "simstudy::missingArgument")
   expect_error(survParamPlot(formula = 4, shape = -1), class = "simstudy::wrongSign")
 })
 
 test_that("survParamPlot works.", {
+  skip_on_cran()
   expect_is(survParamPlot(formula = -4, shape = 1), class = "ggplot")
 
   points <- list(c(100, .8), c(200, .5))