Correct examples using suggests packages to run conditionally

.github/workflows/check-no-suggests.yaml

@@ -0,0 +1,60 @@
+# 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: check-no-suggests.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")'

NAMESPACE

@@ -83,6 +83,7 @@ export(odds)
 export(odds_ratio)
 export(odds_ratio2)
 export(par_pattern)
+export(params)
 export(pbern)
 export(pextreme)
 export(phi)

R/dev.R

@@ -288,11 +288,12 @@ dev_pois_zi <- function(x, lambda, prob = 0, res = FALSE) {
 #' @family dev_dist
 #' @export
 #'
-#' @examples
+#' @examplesIf requireNamespace("sn")
 #' dev_skewnorm(c(-2:2))
 #' dev_skewnorm(-2:2, 0, 1, 5)
 #' dev_skewnorm(-2:2, 0, 1, 5, res = TRUE)
 dev_skewnorm <- function(x, mean = 0, sd = 1, shape = 0, res = FALSE) {
+  rlang::check_installed("sn")
   delta <- shape / sqrt(1 + shape^2)
   mu_z <- sqrt(2 / pi) * delta
   sig_z <- sqrt(1 - mu_z^2)

R/extras-package.R

@@ -2,5 +2,7 @@
 "_PACKAGE"
 
 ## usethis namespace: start
+#' @import chk
+#' @importFrom stats dbinom dlnorm dnorm dpois dnbinom
 ## usethis namespace: end
 NULL

R/fabs.R

@@ -7,6 +7,7 @@
 #'
 #' @param x An existing R object.
 #' @family translations
+#' @return A numeric vector of the corresponding absolute values.
 #' @export
 #' @examples
 #' fabs(c(0, -1, 2))

R/log-lik.R

@@ -214,11 +214,12 @@ log_lik_pois_zi <- function(x, lambda = 1, prob = 0) {
 #' @family log_lik_dist
 #' @export
 #'
-#' @examples
+#' @examplesIf requireNamespace("sn")
 #' log_lik_skewnorm(c(-2:2))
 #' log_lik_skewnorm(c(-2:2), shape = -2)
 #' log_lik_skewnorm(c(-2:2), shape = 2)
 log_lik_skewnorm <- function(x, mean = 0, sd = 1, shape = 0) {
+  rlang::check_installed("sn")
   log_lik <- dskewnorm(x = x, mean = mean, sd = sd, shape = shape, log = TRUE)
   use_norm <- !is.na(shape) & shape == 0
   lnorm <- log_lik_norm(x = x, mean = mean, sd = sd)

R/numericise.R

@@ -77,6 +77,7 @@ numericise.POSIXct <- function(x, ...) {
 #' @examples
 #'
 #' # hms
+#' @examplesIf requireNamespace("hms")
 #' numericise(hms::as_hms("00:01:03"))
 numericise.hms <- function(x, ...) {
   # I'm not sure if this test is needed since S3 function

R/params.R

@@ -50,6 +50,7 @@
 #' @param x An object.
 #' @aliases parameters arguments args
 #' @usage NULL
+#' @export
 # nocov start
 params <- function(...) NULL
 # nocov end

R/ran.R

@@ -180,11 +180,12 @@ ran_pois_zi <- function(n = 1, lambda = 1, prob = 0) {
 #' @family ran_dist
 #' @export
 #'
-#' @examples
+#' @examplesIf requireNamespace("sn")
 #' ran_skewnorm(10, shape = -1)
 #' ran_skewnorm(10, shape = 0)
 #' ran_skewnorm(10, shape = 1)
 ran_skewnorm <- function(n = 1, mean = 0, sd = 1, shape = 0) {
+  rlang::check_installed("sn")
   chk_whole_number(n)
   chk_gte(n)
   rskewnorm(n = n, mean = mean, sd = sd, shape = shape)

R/res.R

@@ -335,9 +335,10 @@ res_student_standardized <- function(x, mean, sd, theta) {
 #' @family res_dist
 #' @export
 #'
-#' @examples
+#' @examplesIf requireNamespace("sn")
 #' res_skewnorm(c(-2:2))
 res_skewnorm <- function(x, mean = 0, sd = 1, shape = 0, type = "dev", simulate = FALSE) {
+  rlang::check_installed("sn")
   chk_string(type)
   if (!vld_false(simulate)) {
     x <- ran_skewnorm(length(x), mean = mean, sd = sd, shape = shape)

R/sens.R

@@ -62,7 +62,7 @@ sens_student <- function(mean, sd, theta, sd_mult = 2) {
 #' @family sens_dist
 #' @export
 #'
-#' @examples
+#' @examplesIf requireNamespace("sn")
 #' sens_skewnorm(10, 3, -1, 2)
 #' sens_skewnorm(10, 3, 3, 0.8)
 sens_skewnorm <- function(mean, sd, shape, sd_mult = 2) {

R/skewnorm.R

@@ -10,7 +10,7 @@
 #' @rdname skewnorm
 #' @export
 #'
-#' @examples
+#' @examplesIf requireNamespace("sn")
 #' dskewnorm(x = -2:2, mean = 0, sd = 1, shape = 0.1)
 #' dskewnorm(x = -2:2, mean = 0, sd = 1, shape = -1)
 #' qskewnorm(p = c(0.1, 0.4), mean = 0, sd = 1, shape = 0.1)
@@ -20,12 +20,7 @@
 #' rskewnorm(n = 3, mean = 0, sd = 1, shape = 0.1)
 #' rskewnorm(n = 3, mean = 0, sd = 1, shape = -1)
 dskewnorm <- function(x, mean = 0, sd = 1, shape = 0, log = FALSE) {
-  if (!requireNamespace("sn", quietly = TRUE)) {
-    stop(
-      "Package \"sn\" must be installed to use this function.",
-      call. = FALSE
-    )
-  }
+  rlang::check_installed("sn")
   chk_gte(sd)
   nulls <- any(is.null(x), is.null(mean), is.null(sd), is.null(shape))
   if (nulls) stop("invalid arguments")
@@ -49,12 +44,7 @@ dskewnorm <- function(x, mean = 0, sd = 1, shape = 0, log = FALSE) {
 #' @rdname skewnorm
 #' @export
 pskewnorm <- function(q, mean = 0, sd = 1, shape = 0) {
-  if (!requireNamespace("sn", quietly = TRUE)) {
-    stop(
-      "Package \"sn\" must be installed to use this function.",
-      call. = FALSE
-    )
-  }
+  rlang::check_installed("sn")
   chk_gte(sd)
   nulls <- any(is.null(q), is.null(mean), is.null(sd), is.null(shape))
   if (nulls) stop("invalid arguments")
@@ -78,12 +68,7 @@ pskewnorm <- function(q, mean = 0, sd = 1, shape = 0) {
 #' @rdname skewnorm
 #' @export
 qskewnorm <- function(p, mean = 0, sd = 1, shape = 0) {
-  if (!requireNamespace("sn", quietly = TRUE)) {
-    stop(
-      "Package \"sn\" must be installed to use this function.",
-      call. = FALSE
-    )
-  }
+  rlang::check_installed("sn")
   chk_gte(sd)
   chk_gte(p)
   chk_lte(p, 1)
@@ -112,12 +97,7 @@ qskewnorm <- function(p, mean = 0, sd = 1, shape = 0) {
 #' @rdname skewnorm
 #' @export
 rskewnorm <- function(n = 1, mean = 0, sd = 1, shape = 0) {
-  if (!requireNamespace("sn", quietly = TRUE)) {
-    stop(
-      "Package \"sn\" must be installed to use this function.",
-      call. = FALSE
-    )
-  }
+  rlang::check_installed("sn")
   chk_gte(n)
   chk_lt(n, Inf)
   chk_not_any_na(n)

cran-comments.md

@@ -1,35 +1,10 @@
-## Test environments
-
-release 4.4.1
-
-* OSX (local) - release
-* OSX (actions) - release
-* OSX (R-hub) - devel
-* Ubuntu (actions) - oldrel-1, release, and devel 
-* Ubuntu (R-hub) - devel
-* Fedora (R-hub)
-* Windows (actions) - release
-* Windows (winbuilder) - devel
-* Windows (R-hub) - devel
-
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
-
-New maintainer:
-  Nicole Hill <[email protected]>
-Old maintainer(s):
-  Joe Thorley <[email protected]>
+0 errors | 0 warnings | 0 notes
 
 ## CRAN Issues
 
-Fixed the following error by conditionally skipping tests that rely on packages listed in suggests, if those packages are not installed.
-After review, also decided to remove the dependency to the 'aods3' package.
-
-══ Failed tests ════════════════════════════════════════════════════════════════
-── Error ('test-log-lik.R:184:3'): beta_binom log_lik ──────────────────────────
-<packageNotFoundError/error/condition>
-Error in `loadNamespace(x)`: there is no package called 'aods3'
+After feedback, corrected the noSuggests issue to have all tests, examples, and vignettes run conditionally for packages listed under Suggests.
 
 ## revdepcheck results
 

inst/WORDLIST

@@ -12,6 +12,7 @@ Summarise
 Surprisal
 TMB
 WinBUGS
+behaviour
 bern
 bigg
 cdot
@@ -24,7 +25,6 @@ lik
 modelling
 numericise
 skewnorm
-styler
 summarise
 surprisal
 testthat