stan-dev · jgabry · Sep 25, 2026 · Sep 24, 2026 · Sep 24, 2026
diff --git a/.github/workflows/R-CMD-check-cran.yaml b/.github/workflows/R-CMD-check-cran.yaml
@@ -0,0 +1,64 @@
+---
+# Check CmdStanR the way CRAN does: NOT_CRAN unset and no CmdStan
+# installed, so only the tests that need neither run.
+# yamllint disable rule:line-length
+
+name: CRAN check
+
+'on':
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+      - v1.0
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  R-CMD-check-cran:
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+    runs-on: ubuntu-latest
+
+    name: ubuntu-latest (release, CRAN)
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      PKG_SYSREQS_DB_UPDATE_TIMEOUT: 30s
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: "always"
+          extra-packages: any::rcmdcheck, local::.
+
+      # setup-r exports NOT_CRAN=true, which would evaluate the vignettes and
+      # run every test; CRAN leaves it unset.
+      - uses: r-lib/actions/check-r-package@v2
+        env:
+          NOT_CRAN: false
+          _R_CHECK_CRAN_INCOMING_: false
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v7
+        with:
+          name: cran-check-results
+          path: check
diff --git a/R/knitr.R b/R/knitr.R
@@ -25,7 +25,7 @@
 #' for an example.
 #'
 #' **Note:** When running chunks interactively in RStudio (e.g. when using
-#' [R Notebooks](https://bookdown.org/yihui/rmarkdown/notebook.html)), it has
+#' [R Notebooks](https://pkg.yihui.org/rmarkdown-book/notebook)), it has
 #' been observed that the built-in, RStan-based engine is used for `stan`
 #' chunks even when CmdStanR's engine has been registered in the session. When
 #' the R Markdown document is knit/rendered, the correct engine is used. As a
@@ -37,8 +37,8 @@
 #' `cmdstan` engine with `override = FALSE`.
 #'
 #' @references
-#' * [Register a custom language engine for knitr](https://bookdown.org/yihui/rmarkdown-cookbook/custom-engine.html)
-#' * [knitr's built-in Stan language engine](https://bookdown.org/yihui/rmarkdown/language-engines.html#stan)
+#' * [Register a custom language engine for knitr](https://pkg.yihui.org/rmarkdown-cookbook/custom-engine)
+#' * [knitr's built-in Stan language engine](https://pkg.yihui.org/rmarkdown-book/language-engines#stan)
 #'
 #' @seealso [eng_cmdstan()]
 #'

diff --git a/man/register_knitr_engine.Rd b/man/register_knitr_engine.Rd
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,6 +1,4 @@
 library(testthat)
 library(cmdstanr)
 
-if (identical(Sys.getenv("NOT_CRAN"), "true")) {
-  test_check("cmdstanr")
-}
+test_check("cmdstanr")
diff --git a/tests/testthat/README.md b/tests/testthat/README.md
@@ -21,6 +21,12 @@ against a mocked CmdStan, so nothing is compiled. `test-model-rebuild.R`
 compiles for real and checks the executable that results from a sequence of
 calls.
 
+Every file that needs CmdStan starts with `skip_on_cran()`, and a test
+that needs CmdStan inside an otherwise pure file calls it itself, so on
+CRAN, where nothing is installed, only the pure R tests run. The
+`CRAN check` workflow runs the suite the same way, with no CmdStan
+installed, so a missing skip fails there rather than on CRAN.
+
 Files that compile call `set_cmdstan_path()` at the top. `with_mocked_cli()`
 in `helper-mock-cli.R` stands in for `make` and for the executable's `info`
 call, so a test can go through the build code without a compiler.

diff --git a/tests/testthat/test-build-info.R b/tests/testthat/test-build-info.R
@@ -324,6 +324,7 @@ test_that("untracked dependencies are ordered by kind and deduplicated", {
 })
 
 test_that("a real user header is reported under dependencies and nowhere else", {
+  skip_on_cran()
   stan_file <- file.path(withr::local_tempdir(), "bernoulli_external.stan")
   file.copy(testing_stan_file("bernoulli_external"), stan_file)
   header <- withr::local_tempfile(

diff --git a/tests/testthat/test-build-record-compile.R b/tests/testthat/test-build-record-compile.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 
 # No C++ is compiled here: the mock writes a text file where make would have

diff --git a/tests/testthat/test-cpp-options.R b/tests/testthat/test-cpp-options.R
@@ -305,6 +305,7 @@ data_file <- test_path("resources", "data", "bernoulli.data.json")
 features <- function(mod) mod$.__enclos_env__$private$reported_features_
 
 test_that("a feature inherited from make/local is reported, not requested", {
+  skip_on_cran()
   stan_file <- file.path(withr::local_tempdir(), "bernoulli.stan")
   file.copy(stan_program, stan_file)
   threaded <- paste0(
@@ -331,6 +332,7 @@ test_that("a feature inherited from make/local is reported, not requested", {
 })
 
 test_that("an executable reporting no threading flag is unknown, not off", {
+  skip_on_cran()
   stan_file <- file.path(withr::local_tempdir(), "bernoulli.stan")
   file.copy(stan_program, stan_file)
   info <- "stan_version_major=2\nstan_version_minor=39\nstan_version_patch=0"
@@ -350,6 +352,7 @@ test_that("an executable reporting no threading flag is unknown, not off", {
 })
 
 test_that("an executable adopted from live info reports threading as unknown", {
+  skip_on_cran()
   stan_file <- file.path(withr::local_tempdir(), "bernoulli.stan")
   file.copy(stan_program, stan_file)
   info <- "stan_version_major=2\nstan_version_minor=39\nstan_version_patch=0"

diff --git a/tests/testthat/test-csv.R b/tests/testthat/test-csv.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 fit_bernoulli_optimize <- testing_fit("bernoulli", method = "optimize", seed = 1234)
 fit_bernoulli_variational <- testing_fit("bernoulli", method = "variational", seed = 123)

diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 fit <- testing_fit("bernoulli", method = "sample", seed = 123)
 fit_vb <- testing_fit("bernoulli", method = "variational", seed = 123)

diff --git a/tests/testthat/test-example.R b/tests/testthat/test-example.R
@@ -12,6 +12,7 @@ stan_program <- "
   "
 
 test_that("cmdstanr_example works", {
+  skip_on_cran()
   fit_mcmc <- cmdstanr_example("logistic", chains = 2, force_recompile = TRUE)
   checkmate::expect_r6(fit_mcmc, "CmdStanMCMC")
   expect_equal(fit_mcmc$num_chains(), 2)

diff --git a/tests/testthat/test-failed-chains.R b/tests/testthat/test-failed-chains.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 stan_program <- testing_stan_file("chain_fails")
 stan_program_init_warnings <- testing_stan_file("init_warnings")

diff --git a/tests/testthat/test-fit-gq.R b/tests/testthat/test-fit-gq.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 fit <- testing_fit("bernoulli", method = "sample", seed = 123)
 fit_gq <- testing_fit("bernoulli_ppc", method = "generate_quantities", seed = 123, fitted_params = fit)

diff --git a/tests/testthat/test-fit-init.R b/tests/testthat/test-fit-init.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 
 data_list_schools <- testing_data("schools")

diff --git a/tests/testthat/test-fit-laplace.R b/tests/testthat/test-fit-laplace.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 fit_laplace <- testing_fit("logistic", method = "laplace", seed = 100)
 PARAM_NAMES <- c("alpha", "beta[1]", "beta[2]", "beta[3]")

diff --git a/tests/testthat/test-fit-mcmc.R b/tests/testthat/test-fit-mcmc.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 fit_mcmc <- testing_fit("logistic", method = "sample",
                         seed = 123, chains = 2, save_metric = FALSE)

diff --git a/tests/testthat/test-fit-mle.R b/tests/testthat/test-fit-mle.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 fit_mle <- testing_fit("logistic", method = "optimize", seed = 123)
 mod <- testing_model("bernoulli")

diff --git a/tests/testthat/test-fit-shared.R b/tests/testthat/test-fit-shared.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 fits <- list()
 fits[["sample"]] <- testing_fit("logistic", method = "sample",

diff --git a/tests/testthat/test-fit-vb.R b/tests/testthat/test-fit-vb.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 fit_vb <- testing_fit("logistic", method = "variational", seed = 123)
 fit_vb_sci_not <- testing_fit("logistic", method = "variational", seed = 123, iter = 200000, adapt_iter = 100000)

diff --git a/tests/testthat/test-install.R b/tests/testthat/test-install.R
@@ -1,4 +1,6 @@
 # avoid parallel on Mac due to strange intermittent TBB errors on Github Actions
+skip_on_cran()
+
 CORES <- if (os_is_macos()) 1 else 2
 
 cmdstan_test_tarball_url <- Sys.getenv("CMDSTAN_TEST_TARBALL_URL")

diff --git a/tests/testthat/test-installation-check.R b/tests/testthat/test-installation-check.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 stan_program <- testing_stan_file("bernoulli")
 

diff --git a/tests/testthat/test-knitr.R b/tests/testthat/test-knitr.R
@@ -5,6 +5,7 @@ test_that("eng_cmdstan throws correct errors", {
 })
 
 test_that("eng_cmdstan works", {
+  skip_on_cran()
   skip_if_not_installed("knitr")
   code <- "
   parameters {

diff --git a/tests/testthat/test-model-cmdstan-defaults.R b/tests/testthat/test-model-cmdstan-defaults.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 mod <- testing_model("bernoulli")
 

diff --git a/tests/testthat/test-model-code-print.R b/tests/testthat/test-model-code-print.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 stan_program <- testing_stan_file("bernoulli")
 mod <- testing_model("bernoulli")

diff --git a/tests/testthat/test-model-compile-user_header.R b/tests/testthat/test-model-compile-user_header.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 local_mocked_stanc <- function(.local_envir = parent.frame()) {
   local_mocked_bindings(
     get_cmdstan_flags = function(flag_name, ...) character(),

diff --git a/tests/testthat/test-model-compile.R b/tests/testthat/test-model-compile.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 stan_program <- cmdstan_example_file()
 local_cmdstan_make_local(cpp_options = list("PRECOMPILED_HEADERS"="false"))

diff --git a/tests/testthat/test-model-data.R b/tests/testthat/test-model-data.R
@@ -1,4 +1,5 @@
 # see separate test-json for testing writing data to JSON
+skip_on_cran()
 
 set_cmdstan_path()
 mod <- testing_model("logistic")

diff --git a/tests/testthat/test-model-diagnose.R b/tests/testthat/test-model-diagnose.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 mod <- testing_model("bernoulli")
 data_list <- testing_data("bernoulli")

diff --git a/tests/testthat/test-model-expose-functions.R b/tests/testthat/test-model-expose-functions.R
@@ -1,4 +1,6 @@
 # Standalone functions not expected to work on WSL yet
+skip_on_cran()
+
 skip_if(os_is_wsl())
 
 set_cmdstan_path()

diff --git a/tests/testthat/test-model-generate_quantities.R b/tests/testthat/test-model-generate_quantities.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 fit <- testing_fit("bernoulli", method = "sample", seed = 123)
 mod_gq <- testing_model("bernoulli_ppc")

diff --git a/tests/testthat/test-model-init.R b/tests/testthat/test-model-init.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 mod <- testing_model("bernoulli")
 data_list <- testing_data("bernoulli")

diff --git a/tests/testthat/test-model-laplace.R b/tests/testthat/test-model-laplace.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 mod <- testing_model("logistic")
 data_list <- testing_data("logistic")

diff --git a/tests/testthat/test-model-methods.R b/tests/testthat/test-model-methods.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 skip_if(os_is_wsl())
 
 set_cmdstan_path()

diff --git a/tests/testthat/test-model-optimize.R b/tests/testthat/test-model-optimize.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 mod <- testing_model("bernoulli")
 data_list <- testing_data("bernoulli")

diff --git a/tests/testthat/test-model-output_dir.R b/tests/testthat/test-model-output_dir.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 
 local_output_sandbox <- function(pattern = "sandbox", .local_envir = parent.frame()) {

diff --git a/tests/testthat/test-model-pathfinder.R b/tests/testthat/test-model-pathfinder.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 stan_program <- testing_stan_file("bernoulli")
 mod <- testing_model("bernoulli")

diff --git a/tests/testthat/test-model-rebuild-rules.R b/tests/testthat/test-model-rebuild-rules.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 
 # The decision cmdstan_model() makes: build, reuse, or adopt. No C++ is

diff --git a/tests/testthat/test-model-rebuild.R b/tests/testthat/test-model-rebuild.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 
 # A fresh copy of a resources/stan/ program (with its include file, for

diff --git a/tests/testthat/test-model-sample-metric.R b/tests/testthat/test-model-sample-metric.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 mod <- testing_model("bernoulli")
 data_list <- testing_data("bernoulli")

diff --git a/tests/testthat/test-model-sample.R b/tests/testthat/test-model-sample.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 stan_program <- testing_stan_file("bernoulli")
 mod <- testing_model("bernoulli")

diff --git a/tests/testthat/test-model-sample_mpi.R b/tests/testthat/test-model-sample_mpi.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("sample_mpi() works", {
   skip_if(!mpi_toolchain_present())
   mpi_file <- write_stan_file("

diff --git a/tests/testthat/test-model-stale-executable.R b/tests/testthat/test-model-stale-executable.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 
 # What R/model.R's private assert_current() and its callers say about every

diff --git a/tests/testthat/test-model-variables.R b/tests/testthat/test-model-variables.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 
 test_that("$variables() work correctly with example models", {

diff --git a/tests/testthat/test-model-variational.R b/tests/testthat/test-model-variational.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 mod <- testing_model("bernoulli")
 data_list <- testing_data("bernoulli")

diff --git a/tests/testthat/test-opencl.R b/tests/testthat/test-opencl.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 set_cmdstan_path()
 fit <- testing_fit("bernoulli", method = "sample", seed = 123, chains = 1)
 

diff --git a/tests/testthat/test-path.R b/tests/testthat/test-path.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 Sys.unsetenv("CMDSTAN")
 PATH <- absolute_path(set_cmdstan_path())
 VERSION <- cmdstan_version()