also check without suggested packages (#306)

* also check without suggested packages

* skips for suggested pkgs

* examples only when engine pkgs available

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

@@ -0,0 +1,57 @@
+# 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:
+    branches: [main, master]
+
+name: R-CMD-check-hard
+
+jobs:
+  R-CMD-check:
+    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@v3
+
+      - 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

R/bag_tree-rpart.R

@@ -4,7 +4,7 @@
 #' @return A vector.
 #' @keywords internal
 #' @export
-#' @examples
+#' @examplesIf rlang::is_installed("ipred")
 #' bagged_tree <- bag_tree() %>%
 #'   set_engine("rpart") %>%
 #'   set_mode("censored regression") %>%
@@ -61,7 +61,7 @@ get_missings_survbagg <- function(object, new_data) {
 #' @return A vctrs list of tibbles.
 #' @keywords internal
 #' @export
-#' @examples
+#' @examplesIf rlang::is_installed("ipred")
 #' bagged_tree <- bag_tree() %>%
 #'   set_engine("rpart") %>%
 #'   set_mode("censored regression") %>%

R/boost_tree-mboost.R

@@ -31,7 +31,7 @@
 #' @return A fitted blackboost model.
 #' @keywords internal
 #' @export
-#' @examples
+#' @examplesIf rlang::is_installed("mboost")
 #' blackboost_train(Surv(time, status) ~ age + ph.ecog,
 #'   data = lung[-14, ], family = mboost::CoxPH()
 #' )
@@ -111,7 +111,7 @@ predict_linear_pred._blackboost <- function(object,
 #' @return A tibble with a list column of nested tibbles.
 #' @keywords internal
 #' @export
-#' @examples
+#' @examplesIf rlang::is_installed("mboost")
 #' mod <- boost_tree() %>%
 #'   set_engine("mboost") %>%
 #'   set_mode("censored regression") %>%
@@ -176,7 +176,7 @@ survival_curve_to_prob <- function(eval_time, event_times, survival_prob) {
 #' @return A tibble.
 #' @keywords internal
 #' @export
-#' @examples
+#' @examplesIf rlang::is_installed("mboost")
 #' boosted_tree <- boost_tree() %>%
 #'   set_engine("mboost") %>%
 #'   set_mode("censored regression") %>%

R/decision_tree-rpart.R

@@ -5,7 +5,7 @@
 #' @return A tibble with a list column of nested tibbles.
 #' @keywords internal
 #' @export
-#' @examples
+#' @examplesIf rlang::is_installed("pec")
 #' mod <- decision_tree() %>% 
 #'   set_mode("censored regression") %>%
 #'     set_engine("rpart") %>%

R/partykit.R

@@ -9,7 +9,7 @@
 #' @return A tibble with a list column of nested tibbles.
 #' @export
 #' @keywords internal
-#' @examples
+#' @examplesIf rlang::is_installed(c("partykit", "coin"))
 #' tree <- decision_tree() %>%
 #'   set_mode("censored regression") %>%
 #'   set_engine("partykit") %>%

R/proportional_hazards-glmnet.R

@@ -23,7 +23,7 @@
 #' @return A fitted `glmnet` model.
 #' @export
 #' @keywords internal
-#' @examples
+#' @examplesIf rlang::is_installed("glmnet")
 #' coxnet_mod <- coxnet_train(Surv(time, status) ~ age + sex, data = lung)
 coxnet_train <- function(formula,
                          data,
@@ -471,7 +471,7 @@ multi_predict_coxnet_linear_pred <- function(object, new_data, opts, penalty) {
 #' @return A vector.
 #' @keywords internal
 #' @export
-#' @examples
+#' @examplesIf rlang::is_installed("glmnet")
 #' cox_mod <- proportional_hazards(penalty = 0.1) %>%
 #'   set_engine("glmnet") %>%
 #'   fit(Surv(time, status) ~ ., data = lung)
@@ -596,7 +596,7 @@ get_missings_coxnet <- function(new_x, new_strata) {
 #' @return A tibble with a list column of nested tibbles.
 #' @keywords internal
 #' @export
-#' @examples
+#' @examplesIf rlang::is_installed("glmnet")
 #' cox_mod <- proportional_hazards(penalty = 0.1) %>%
 #'   set_engine("glmnet") %>%
 #'   fit(Surv(time, status) ~ ., data = lung)

R/rand_forest-aorsf.R

@@ -8,7 +8,7 @@
 #' @export
 #' @keywords internal
 #' @name aorsf_internal
-#' @examples
+#' @examplesIf rlang::is_installed("aorsf")
 #' mod <- rand_forest() %>%
 #'   set_engine("aorsf") %>%
 #'   set_mode("censored regression") %>%

README.Rmd

@@ -19,6 +19,7 @@ knitr::opts_chunk$set(
 [![R-CMD-check](https://github.com/tidymodels/censored/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tidymodels/censored/actions/workflows/R-CMD-check.yaml)
 [![Codecov test coverage](https://codecov.io/gh/tidymodels/censored/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tidymodels/censored?branch=main)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html) 
+[![R-CMD-check-hard](https://github.com/tidymodels/censored/actions/workflows/R-CMD-check-hard.yaml/badge.svg)](https://github.com/tidymodels/censored/actions/workflows/R-CMD-check-hard.yaml)
 <!-- badges: end -->
 
 `censored` is a [parsnip](https://parsnip.tidymodels.org) extension package which provides engines for various models for censored regression and survival analysis.

README.md

@@ -10,6 +10,7 @@
 coverage](https://codecov.io/gh/tidymodels/censored/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tidymodels/censored?branch=main)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html)
+[![R-CMD-check-hard](https://github.com/tidymodels/censored/actions/workflows/R-CMD-check-hard.yaml/badge.svg)](https://github.com/tidymodels/censored/actions/workflows/R-CMD-check-hard.yaml)
 <!-- badges: end -->
 
 `censored` is a [parsnip](https://parsnip.tidymodels.org) extension

tests/testthat/test-bag_tree-rpart.R

@@ -87,6 +87,7 @@ test_that("time predictions without surrogate splits for NA", {
 })
 
 test_that("survival_time_survbagg() throws an informative error with an engine object", {
+  skip_if_not_installed("ipred")
   mod <- ipred::bagging(Surv(time, status) ~ age + ph.ecog, data = lung)
   expect_snapshot(error = TRUE, {
     survival_time_survbagg(mod)

tests/testthat/test-proportional_hazards-survival.R

@@ -156,6 +156,7 @@ test_that("prediction from stratified models require strata variables in new_dat
 # prediction: survival ----------------------------------------------------
 
 test_that("survival predictions without strata", {
+  skip_if_not_installed("pec")
   # due to pec:
   skip_if_not_installed("Matrix", minimum_version = "1.4.2")