"noSuggests" R CMD check (#79)

* "noSuggests" R CMD check

* change name

* updates for no-suggests

* skip_if_not_installed("modeldata")

* @#%!

.github/workflows/R-CMD-check-hard.yaml

@@ -0,0 +1,59 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# NOTE: This workflow only directly installs "hard" dependencies, i.e. Depends,
+# Imports, and LinkingTo dependencies. Notably, Suggests dependencies are never
+# installed, with the exception of testthat, knitr, and rmarkdown. The cache is
+# never used to avoid accidentally restoring a cache containing a suggested
+# dependency.
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: R-CMD-check-hard.yaml
+
+permissions: read-all
+
+jobs:
+  check-no-suggests:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: '"hard"'
+          cache: false
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::knitr
+            any::rmarkdown
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

R/bagger.R

@@ -44,49 +44,50 @@
 #' comparison of methods to study the contribution of variables in artificial
 #' neural network models. Ecological Modelling, 160(3), 249-264.
 #' @examples
-#' library(recipes)
-#' library(dplyr)
+#' if (rlang::is_installed(c("recipes", "modeldata"))) {
+#'   library(recipes)
+#'   library(dplyr)
 #'
-#' data(biomass, package = "modeldata")
+#'   data(biomass, package = "modeldata")
 #'
-#' biomass_tr <-
-#'   biomass %>%
-#'   dplyr::filter(dataset == "Training") %>%
-#'   dplyr::select(-dataset, -sample)
+#'   biomass_tr <-
+#'     biomass %>%
+#'     dplyr::filter(dataset == "Training") %>%
+#'     dplyr::select(-dataset, -sample)
 #'
-#' biomass_te <-
-#'   biomass %>%
-#'   dplyr::filter(dataset == "Testing") %>%
-#'   dplyr::select(-dataset, -sample)
+#'   biomass_te <-
+#'     biomass %>%
+#'     dplyr::filter(dataset == "Testing") %>%
+#'     dplyr::select(-dataset, -sample)
 #'
-#' # ------------------------------------------------------------------------------
+#'   # ------------------------------------------------------------------------------
 #'
-#' ctrl <- control_bag(var_imp = TRUE)
+#'   ctrl <- control_bag(var_imp = TRUE)
 #'
-#' # ------------------------------------------------------------------------------
+#'   # ------------------------------------------------------------------------------
 #'
-#' # `times` is low to make the examples run faster
+#'   # `times` is low to make the examples run faster
 #'
 #'
-#' set.seed(7687)
-#' cart_bag <- bagger(x = biomass_tr[, -6], y = biomass_tr$HHV,
-#'                    base_model = "CART", times = 5, control = ctrl)
-#' cart_bag
-#'
-#' # ------------------------------------------------------------------------------
-#' # Other interfaces
+#'   set.seed(7687)
+#'   cart_bag <- bagger(x = biomass_tr[, -6], y = biomass_tr$HHV,
+#'                      base_model = "CART", times = 5, control = ctrl)
+#'   cart_bag
 #'
-#' # Recipes can be used
-#' biomass_rec <-
-#'   recipe(HHV ~ ., data = biomass_tr) %>%
-#'   step_pca(all_predictors())
+#'   # ------------------------------------------------------------------------------
+#'   # Other interfaces
 #'
-#' set.seed(7687)
-#' cart_pca_bag <- bagger(biomass_rec, data = biomass_tr, base_model = "CART",
-#'                        times = 5, control = ctrl)
+#'   # Recipes can be used
+#'   biomass_rec <-
+#'     recipe(HHV ~ ., data = biomass_tr) %>%
+#'     step_pca(all_predictors())
 #'
-#' cart_pca_bag
+#'   set.seed(7687)
+#'   cart_pca_bag <- bagger(biomass_rec, data = biomass_tr, base_model = "CART",
+#'                          times = 5, control = ctrl)
 #'
+#'   cart_pca_bag
+#' }
 #' @export
 bagger <- function(x, ...) {
   UseMethod("bagger")

tests/testthat/helper-baguette.R

@@ -1,9 +1,14 @@
 library(rlang)
 library(purrr)
-library(yardstick)
-library(recipes)
-
-data("two_class_dat", package = "modeldata")
+if (is_installed("yardstick")) {
+  library(yardstick)
+}
+if (is_installed("recipes")) {
+  library(recipes)
+}
+if (is_installed("modeldata")) {
+  data("two_class_dat", package = "modeldata")
+}
 
 # ------------------------------------------------------------------------------
 

tests/testthat/test-C5.R

@@ -66,6 +66,7 @@ test_that('check model reduction', {
 # ------------------------------------------------------------------------------
 
 test_that('check C5 parsnip interface', {
+  skip_if_not_installed("modeldata")
 
   set.seed(4779)
   expect_error(

tests/testthat/test-cart.R

@@ -1,4 +1,5 @@
 test_that('check CART opt', {
+  skip_if_not_installed("modeldata")
 
   mod_1 <-
     bagger(
@@ -99,6 +100,8 @@ test_that('check model reduction', {
 # ------------------------------------------------------------------------------
 
 test_that('check CART parsnip interface', {
+  skip_if_not_installed("modeldata")
+
   set.seed(4779)
   expect_error(
     reg_mod <- bag_tree(cost_complexity = .001, min_n = 3) %>%
@@ -204,6 +207,7 @@ test_that('mode specific package dependencies', {
 
 test_that('case weights', {
   skip_if_not_installed("modeldata")
+
   data("two_class_dat", package = "modeldata")
   set.seed(1)
   wts <- runif(nrow(two_class_dat))

tests/testthat/test-interfaces.R

@@ -1,4 +1,6 @@
 test_that('recipe execution', {
+  skip_if_not_installed("recipes")
+
   # check to make sure that prepped data are given to model
   rec <-
     recipe(Sepal.Length ~ ., data = iris) %>%

tests/testthat/test-mars.R

@@ -1,5 +1,7 @@
 test_that('check mars opt', {
   skip_if_not_installed("earth")
+  skip_if_not_installed("modeldata")
+
   set.seed(36323)
   check_pruning <- function(x, ...) {
     rlang::eval_tidy(x$call$pmethod) == "backward"
@@ -91,6 +93,8 @@ test_that('check model reduction', {
 
 test_that('check MARS parsnip interface', {
   skip_if_not_installed("earth")
+  skip_if_not_installed("modeldata")
+
   set.seed(4779)
   expect_error(
     reg_mod <- bag_mars(num_terms = 5, prod_degree = 2) %>%

tests/testthat/test-nnet.R

@@ -1,6 +1,8 @@
 
 test_that('check nnet parsnip interface', {
   skip_if_not_installed("nnet")
+  skip_if_not_installed("modeldata")
+
   data(two_class_dat, package = "modeldata")
 
   set.seed(4779)

tests/testthat/test-validation.R

@@ -88,6 +88,8 @@ test_that('validate imps', {
 
 test_that('bad inputs', {
   skip_if_not_installed("earth")
+  skip_if_not_installed("modeldata")
+
   expect_error(
     bagger(mpg ~ ., data = mtcars, base_model = letters[1:2]),
     "should be a single character value."