fix all skipped tests

R/caretList.R

@@ -88,7 +88,7 @@ trControlCheck <- function(x, y) {
     stop("Please pass exactly 1 argument to savePredictions, e.g. savePredictions='final'")
   }
 
-  if (x$savePredictions) {
+  if (x$savePredictions %in% c(TRUE)) {
     warning("x$savePredictions == TRUE is depreciated. Setting to 'final' instead.")
     x$savePredictions <- "final"
   }

R/helper_functions.R

@@ -259,10 +259,7 @@ extractModelTypes <- function(list_of_models) {
 #' @importFrom data.table data.table setorderv
 bestPreds <- function(x) {
   stopifnot(is(x, "train"))
-  stopifnot({
-    x$control$savePredictions %in% c("all", "final") |
-      x$control$savePredictions
-  })
+  stopifnot(x$control$savePredictions %in% c("all", "final", TRUE))
   a <- data.table(x$bestTune, key = names(x$bestTune))
   b <- data.table(x$pred, key = names(x$bestTune))
   b <- b[a, ]

tests/testthat/test-a-skip.R

@@ -1,10 +1,9 @@
 context("Test skips are working correctly")
 test_that("Skips work correctly", {
   skip("Basic skip failed")
+  expect_equal(1, 0)
 })
-test_that("Skips work correctly", {
-  skip_on_travis()
-})
-test_that("Skips work correctly", {
+test_that("Skips work correctly on CRAN", {
   skip_on_cran()
+  expect_equal(1, 1)
 })

tests/testthat/test-caretStack.R

@@ -1,4 +1,3 @@
-context("Does stacking and prediction work?")
 library(caret)
 
 data(models.reg)
@@ -9,6 +8,9 @@ data(models.class)
 data(X.class)
 data(Y.class)
 
+
+context("Does stacking and prediction work?")
+
 test_that("We can stack regression models", {
   set.seed(96367)
   ens.reg <- caretStack(
@@ -43,7 +45,6 @@ test_that("We can stack classification models", {
 })
 
 test_that("caretStack plots", {
-  skip_if_not_installed("gbm")
   test_plot_file <- "caretEnsemble_test_plots.png"
   ens.reg <- caretStack(
     models.reg,
@@ -55,6 +56,7 @@ test_that("caretStack plots", {
   dotplot(ens.reg, metric = "RMSE")
   dev.off()
   unlink(test_plot_file)
+  expect_is(ens.reg, "caretStack")
 })
 
 context("Prediction errors for caretStack work as expected")

tests/testthat/test-ensembleMethods.R

@@ -29,22 +29,21 @@ test_that("We can get variable importance in ensembles", {
   expect_is(varImp(ens.reg, scale = TRUE, weight = TRUE), "data.frame")
 })
 
-test_that("We get warnings when scale is set to FALSE and weight is TRUE", {
-  skip_on_cran()
+test_that("varImp works for caretEnsembles", {
   set.seed(2239)
-  ens.class <- caretEnsemble(models.class, trControl = trainControl(method = "none"))
-  # varImp struggles with the rf in our test suite, why?
-  models.subset <- models.reg[2:4]
-  class(models.subset) <- "caretList"
-  ens.reg <- caretEnsemble(models.subset, trControl = trainControl(method = "none"))
-  i <- varImp(ens.reg, scale = FALSE, weight = TRUE)
-  i <- varImp(ens.class, scale = FALSE, weight = TRUE)
-  i <- varImp(ens.reg, scale = FALSE, weight = TRUE)
-  i <- varImp(ens.class, scale = FALSE, weight = TRUE)
-  i <- varImp(ens.reg, scale = FALSE)
-  i <- varImp(ens.class, scale = FALSE)
-  i <- varImp(ens.reg, scale = FALSE)
-  i <- varImp(ens.class, scale = FALSE)
+  for (models in list(models.class, models.reg)) {
+    ens <- caretEnsemble(models, trControl = trainControl(method = "none"))
+    expected_names <- c("overall", names(ens$models))
+    expected_row_names <- c("Intercept", "Speciesversicolor", "Speciesvirginica", "Petal.Width", "Sepal.Width", "Petal.Length")
+    for (s in c(TRUE, FALSE)) {
+      for (w in c(TRUE, FALSE)) {
+        i <- varImp(ens, scale = s, weight = w)
+        expect_is(i, "data.frame")
+        expect_equal(names(i), expected_names)
+        expect_equal(row.names(i), expected_row_names)
+      }
+    }
+  }
 })
 
 test_that("We get the right dimensions back", {

tests/testthat/test-helper_functions.R

@@ -110,8 +110,8 @@ w1 <- c(0.1, 0.1, 0.1, 0.7)
 
 test_that("wtd.sd applies weights correctly", {
   expect_error(caretEnsemble:::wtd.sd(x))
-  expect_false(sd(x1) == wtd.sd(x1, w = x2))
-  expect_false(sd(x1) == wtd.sd(x1, w = x2))
+  expect_false(sd(x1) == caretEnsemble:::wtd.sd(x1, w = x2))
+  expect_false(sd(x1) == caretEnsemble:::wtd.sd(x1, w = x2))
   expect_equal(caretEnsemble:::wtd.sd(y, w = w1), 7.84, tolerance = .001)
   expect_equal(caretEnsemble:::wtd.sd(y, w = w1 * 100), caretEnsemble:::wtd.sd(y, w = w1))
 })
@@ -131,7 +131,6 @@ test_that("wtd.sd handles NA values correctly", {
 
 test_that("Checks generate errors", {
   skip_on_cran()
-  skip_if_not_installed("rpart")
   set.seed(42)
   myControl <- trainControl(method = "cv", number = 5, savePredictions = "final")
   suppressWarnings(

tests/testthat/test-parallel.R

@@ -3,6 +3,7 @@
 context("Parallelization works")
 test_that("predict.caretEnsemble works in parallel", {
   skip_on_cran()
+  pbapply::pboptions(type = "none")
   X_reg <- model.matrix(~., iris[, -1])
   X_reg_big <- do.call(rbind, lapply(1:100, function(x) X_reg))
   Y_reg <- iris[, 1]