update for new CRAN policies

Author: pfistfl

DESCRIPTION

@@ -47,6 +47,7 @@ Imports:
     mlr3misc (>= 0.8.0),
     mlr3pipelines (>= 0.3.0),
     R6 (>= 2.4.1),
+    rmarkdown,
     rpart,
     glmnet
 Suggests:
@@ -61,7 +62,6 @@ Suggests:
     paradox,
     knitr,
     ranger,
-    rmarkdown,
     xgboost,
     covr,
     testthat (>= 3.1.0)

NAMESPACE

@@ -21,6 +21,7 @@ import(glmnet)
 import(mlr3)
 import(mlr3misc)
 import(mlr3pipelines)
+import(rmarkdown)
 import(rpart)
 importFrom(R6,R6Class)
 importFrom(R6,is.R6)

R/zzz.R

@@ -5,6 +5,7 @@
 #' @import glmnet
 #' @import rpart
 #' @import mlr3pipelines
+#' @import rmarkdown
 #' @importFrom R6 R6Class is.R6
 #' @importFrom utils head
 #' @importFrom stats contrasts runif rnorm  setNames quantile

tests/testthat/test_auditor_fitters.R

@@ -16,6 +16,7 @@ test_that("LearnerAuditorFitters work", {
 })
 
 test_that("TreeAuditorFitters work", {
+  skip_if_not_installed("mlr3learners")
   skip_if_not_installed("rpart")
   rf = TreeAuditorFitter$new()
   out = rf$fit(iris[, 1:4], runif(150))

tests/testthat/test_cv_predictors.R

@@ -2,6 +2,7 @@ skip_if_not_installed("mlr3")
 
 test_that("TreeAuditorFitters work", {
   skip_on_cran()
+  skip_if_not_installed("mlr3learners")
   skip_if_not_installed("rpart")
   rf = CVTreeAuditorFitter$new()
   out = rf$fit(iris[, 1:4], runif(150))
@@ -14,6 +15,8 @@ test_that("TreeAuditorFitters work", {
 
 test_that("MCBoost multicalibrate and predict_probs - CV Predictor", {
   skip_on_cran()
+  skip_if_not_installed("mlr3learners")
+  skip_if_not_installed("rpart")
   # Sonar task
   tsk = tsk("sonar")
   data = tsk$data(cols = tsk$feature_names)
@@ -31,6 +34,8 @@ test_that("MCBoost multicalibrate and predict_probs - CV Predictor", {
 
 test_that("Creating own CV Predictor works with different folds", {
   skip_on_cran()
+  skip_if_not_installed("mlr3learners")
+  skip_if_not_installed("rpart")
   # Sonar task
   tsk = tsk("sonar")
   data = tsk$data(cols = tsk$feature_names)

tests/testthat/test_mcboost.R

@@ -1,14 +1,14 @@
 skip_if_not_installed("mlr3")
 
 test_that("MCBoost class instantiation", {
+  skip_on_cran()
   mc = MCBoost$new(auditor_fitter = "TreeAuditorFitter")
   expect_class(mc, "MCBoost")
   expect_class(mc$auditor_fitter, "AuditorFitter")
   expect_function(mc$predictor, args = "data")
 
 })
 
-
 test_that("MCBoost multicalibrate and predict_probs - ConstantPredictor", {
   skip_on_cran()
   # Sonar task
@@ -26,7 +26,6 @@ test_that("MCBoost multicalibrate and predict_probs - ConstantPredictor", {
   expect_numeric(prds, lower = 0, upper = 1, len = nrow(data))
 })
 
-
 test_that("MCBoost multicalibrate and predict_probs - init_predictor function", {
   skip_on_cran()
   # Sonar task
@@ -63,7 +62,6 @@ test_that("MCBoost multicalibrate and predict_probs - init_predictor function",
 
 })
 
-
 test_that("MCBoost multicalibrate and predict_probs - Init trained LearnerPredictor - response", {
   skip_on_cran()
   # Sonar task
@@ -84,7 +82,6 @@ test_that("MCBoost multicalibrate and predict_probs - Init trained LearnerPredic
   expect_numeric(prds, lower = 0, upper = 1, len = nrow(data))
 })
 
-
 test_that("MCBoost multicalibrate and predict_probs - Init trained LearnerPredictor - prob", {
   skip_on_cran()
   # Breast Cancer task
@@ -105,7 +102,6 @@ test_that("MCBoost multicalibrate and predict_probs - Init trained LearnerPredic
   expect_numeric(prds, lower = 0, upper = 1, len = nrow(data))
 })
 
-
 test_that("MCBoost multicalibrate with subpops", {
   skip_on_os("solaris")
   skip_on_cran()
@@ -163,6 +159,8 @@ test_that("MCBoost multicalibrate with subpops", {
 test_that("MCBoost various settings", {
   skip_on_cran()
   skip_on_os("solaris")
+  skip_if_not_installed("mlr3learners")
+  skip_if_not_installed("rpart")
   # Sonar task
   tsk = tsk("sonar")
   data = tsk$data(cols = tsk$feature_names)
@@ -199,7 +197,6 @@ test_that("MCBoost various settings", {
   expect_numeric(prd, lower = 0, upper = 1, len = nrow(data))
 })
 
-
 test_that("MCBoost Edge Cases", {
   skip_on_cran()
   # Sonar task
@@ -231,6 +228,8 @@ test_that("MCBoost Edge Cases", {
 
 test_that("MCBoost args for self-defined init predictor", {
   skip_on_os("solaris")
+  skip_if_not_installed("mlr3learners")
+  skip_if_not_installed("ranger")
   # Sonar task
   tsk = tsk("sonar")
   data = tsk$data(cols = tsk$feature_names)
@@ -293,6 +292,9 @@ test_that("MCBoost throws error if wrong auditor_fitter", {
 
 test_that("init predictor wrapper works", {
   skip_on_cran()
+  skip_if_not_installed("mlr3learners")
+  skip_if_not_installed("ranger")
+
   # sonar task
   tsk = tsk("sonar")
   d = tsk$data(cols = tsk$feature_names, rows = c(1:10, 200:208))
@@ -328,8 +330,11 @@ test_that("init predictor wrapper works", {
 })
 
 test_that("mcboost on training data sanity checks", {
-  skip_on_os("solaris")
   skip_on_cran()
+  skip_on_os("solaris")
+  skip_if_not_installed("mlr3learners")
+  skip_if_not_installed("rpart")
+
   tsk = tsk("sonar")
   d = tsk$data(cols = tsk$feature_names)
   l = tsk$data(cols = tsk$target_names)[[1]]

tests/testthat/test_pipeop_mcboost.R

@@ -3,8 +3,9 @@ skip_if_not_installed("mlr3")
 test_that("MCBoost class instantiation", {
   skip_on_cran()
   skip_on_os("solaris")
-  skip_if_not(require("mlr3"))
-  skip_if_not(require("mlr3pipelines"))
+  skip_if_not_installed("mlr3")
+  skip_if_not_installed("mlr3learners")
+  skip_if_not_installed("mlr3pipelines")
   gr = gunion(list(
     "data" = po("nop"),
     "prediction" = po("learner_cv", lrn("classif.rpart"))
@@ -24,6 +25,8 @@ test_that("MCBoost class instantiation", {
 test_that("pipeop instantiation", {
   skip_on_cran()
   skip_on_os("solaris")
+  skip_if_not_installed("mlr3")
+  skip_if_not_installed("mlr3pipelines")
   pop = po("mcboost")
   expect_is(pop, "PipeOpMCBoost")
   expect_is(pop, "PipeOp")
@@ -34,8 +37,9 @@ test_that("pipeop instantiation", {
 test_that("MCBoost ppl", {
   skip_on_cran()
   skip_on_os("solaris")
-  skip_if_not(require("mlr3"))
-  skip_if_not(require("mlr3pipelines"))
+  skip_if_not_installed("mlr3")
+  skip_if_not_installed("mlr3learners")
+  skip_if_not_installed("mlr3pipelines")
 
   l = lrn("classif.featureless")$train(tsk("sonar"))
   pp = ppl_mcboost()
@@ -50,6 +54,10 @@ test_that("MCBoost ppl", {
 test_that("MCBoostSurv ppl", {
   skip_on_cran()
   skip_on_os("solaris")
+  skip_if_not_installed("mlr3")
+  skip_if_not_installed("mlr3learners")
+  skip_if_not_installed("mlr3pipelines")
+  skip_on_os("solaris")
   gr = ppl_mcboost(lrn("classif.rpart"))
   expect_is(gr, "Graph")
 })

tests/testthat/test_predictor.R

@@ -19,6 +19,7 @@ test_that("ConstantPredictor", {
 
 test_that("LearnerPredictor - response", {
   skip_on_cran()
+  skip_if_not_installed("mlr3learners") 
   prd = LearnerPredictor$new(lrn("classif.rpart"))
   expect_class(prd, "LearnerPredictor")
   prd$fit(iris[1:100,1:4], factor(iris$Species[1:100]))
@@ -29,6 +30,7 @@ test_that("LearnerPredictor - response", {
 
 test_that("LearnerPredictor - probs", {
   skip_on_cran()
+  skip_if_not_installed("mlr3learners") 
   prd = LearnerPredictor$new(lrn("classif.rpart", predict_type = "prob"))
   expect_class(prd, "LearnerPredictor")
   prd$fit(iris[51:150,1:4], factor(iris$Species[51:150]))

tests/testthat/test_probrange.R

@@ -1,5 +1,3 @@
-skip_if_not_installed("mlr3")
-
 test_that("ProbRange works", {
   skip_on_cran()
   pr = ProbRange$new(0.1, 0.55)

tests/testthat/test_sonar_usecase.R

@@ -2,6 +2,7 @@ skip_if_not_installed("mlr3")
 
 test_that("TreeAuditorFitters work", {
   skip_on_cran()
+  skip_if_not_installed("mlr3learners") 
   skip_if_not_installed("rpart")
   tsk = tsk("sonar")
   data = tsk$data()[, Class := as.integer(Class) - 1L]