ensure purl'd vignette code can be executed, closes #328

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

@@ -20,16 +20,19 @@ jobs:
       matrix:
         config:
 # running Windows and Mac with --no-examples to avoid spurious Stan crashes in examples
-          - {os: windows-latest, r: 'release', suffix: 'quick', not_cran: 'false', check_options: '"--no-build-vignettes", "--ignore-vignettes", "--no-examples"'}
-          - {os: macOS-latest, r: 'release', suffix: 'quick', not_cran: 'false', check_options: '"--no-build-vignettes", "--ignore-vignettes", "--no-examples"'}
-          - {os: macOS-latest, r: 'release', suffix: '', not_cran: 'true', check_options: 'NULL'}
-          - {os: ubuntu-latest, r: 'devel', suffix: '', not_cran: 'true', check_options: 'NULL', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: 'release'}
-          - {os: ubuntu-latest, r: 'release', suffix: '', not_cran: 'true', check_options: 'NULL', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-latest, r: 'release', suffix: 'quick', not_cran: 'false', check_options: '"--no-build-vignettes", "--ignore-vignettes"', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-latest, r: 'oldrel-1', suffix: 'quick', not_cran: 'false', check_options: '"--no-build-vignettes", "--ignore-vignettes"', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-latest, r: 'oldrel-2', suffix: 'quick', not_cran: 'false', check_options: '"--no-build-vignettes", "--ignore-vignettes"', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-latest, r: 'oldrel-3', suffix: 'quick', not_cran: 'false', check_options: '"--no-build-vignettes", "--ignore-vignettes"', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-latest, r: 'oldrel-4', suffix: 'quick', not_cran: 'false', check_options: '"--no-build-vignettes", "--ignore-vignettes"', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: windows-latest, r: 'release', suffix: 'quick', not_cran: 'false', check_options: '"--as-cran", "--no-build-vignettes", "--ignore-vignettes", "--no-examples"'}
+          - {os: macOS-latest, r: 'release', suffix: 'quick', not_cran: 'false', check_options: '"--as-cran", "--no-build-vignettes", "--ignore-vignettes", "--no-examples"'}
+# running Mac without --as-cran and with --no-build-vignettes only to check that purl'd code from vignettes is runnable (#328)
+          - {os: macOS-latest, r: 'release', suffix: 'purl', not_cran: 'true', check_options: '"--no-build-vignettes"'}
+# full checks on linux
+          - {os: ubuntu-latest, r: 'devel', suffix: '', not_cran: 'true', check_options: '"--as-cran"', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: 'release'}
+          - {os: ubuntu-latest, r: 'release', suffix: '', not_cran: 'true', check_options: '"--as-cran"', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+# quick checks on linux
+          - {os: ubuntu-latest, r: 'release', suffix: 'quick', not_cran: 'false', check_options: '"--as-cran", "--no-build-vignettes", "--ignore-vignettes"', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-latest, r: 'oldrel-1', suffix: 'quick', not_cran: 'false', check_options: '"--as-cran", "--no-build-vignettes", "--ignore-vignettes"', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-latest, r: 'oldrel-2', suffix: 'quick', not_cran: 'false', check_options: '"--as-cran", "--no-build-vignettes", "--ignore-vignettes"', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-latest, r: 'oldrel-3', suffix: 'quick', not_cran: 'false', check_options: '"--as-cran", "--no-build-vignettes", "--ignore-vignettes"', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-latest, r: 'oldrel-4', suffix: 'quick', not_cran: 'false', check_options: '"--as-cran", "--no-build-vignettes", "--ignore-vignettes"', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -80,7 +83,7 @@ jobs:
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
           NOT_CRAN: ${{ matrix.config.not_cran }}
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", ${{ matrix.config.check_options }}), error_on = "warning", check_dir = "check")
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", ${{ matrix.config.check_options }}), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
       - name: Upload check results

NEWS.md

@@ -1,13 +1,15 @@
 # tidybayes (development version)
 
+* Ensure vignette code run through `knitr::purl()` can be executed. (#328)
+
+
 # tidybayes 3.0.7
 
 New features:
 
 * Add support for `draw_indices` parameter in `spread_draws()` and
   `gather_draws()`. (#323)
 
-
 Bug fixes:
 
 * Support for matrix columns in `nest_rvars()` and `unnest_rvars()`. (#316)

vignettes/children/chunk_options.txt

@@ -26,7 +26,8 @@ eval_chunks = identical(Sys.getenv("NOT_CRAN"), "true")
 knitr::opts_chunk$set(
   fig.width = small_width,
   fig.height = small_height,
-  eval = eval_chunks
+  eval = eval_chunks,
+  purl = eval_chunks
 )
 if (capabilities("cairo") && Sys.info()[['sysname']] != "Darwin") {
   knitr::opts_chunk$set(

vignettes/tidybayes.Rmd

@@ -133,7 +133,48 @@ Shunting data from a data frame into a format usable in samplers like JAGS or St
 
 A hierarchical model of our example data might fit an overall mean across the conditions (`overall_mean`), the standard deviation of the condition means (`condition_mean_sd`), the mean within each condition (`condition_mean[condition]`) and the standard deviation of the responses given a condition mean (`response_sd`):
 
-```{stan ABC_stan_model, output.var = "ABC_stan", results = "hide"}
+```{r ABC_stan_model_R, include = FALSE}
+# a stupid workaround for the fact that knitr::purl() will not generate an
+# R script that can be executed from top to bottom if a vignette contains a stan
+# code block (i.e. the very next code block), and some R CMD CHECK configurations
+# unreasonably expect that it can. (see https://stat.ethz.ch/pipermail/r-devel/2014-May/069113.html)
+
+# so for now we'll just do this in R code behind the scenes, even though the best
+# solution would be that people don't run R CMD CHECK with those configurations 
+# (most configurations on CRAN have this problem except macos on R 4.3
+# for some reason, which as of 9/16/2024 appears to be configured differently
+# from other platforms). See https://github.com/mjskay/tidybayes/issues/328
+ABC_stan = stan_model(model_code = '
+  data {
+    int<lower=1> n;
+    int<lower=1> n_condition;
+    int<lower=1, upper=n_condition> condition[n];
+    real response[n];
+  }
+  parameters {
+    real overall_mean;
+    vector[n_condition] condition_zoffset;
+    real<lower=0> response_sd;
+    real<lower=0> condition_mean_sd;
+  }
+  transformed parameters {
+    vector[n_condition] condition_mean;
+    condition_mean = overall_mean + condition_zoffset * condition_mean_sd;
+  }
+  model {
+    response_sd ~ cauchy(0, 1);         // => half-cauchy(0, 1)
+    condition_mean_sd ~ cauchy(0, 1);   // => half-cauchy(0, 1)
+    overall_mean ~ normal(0, 5);
+    condition_zoffset ~ normal(0, 1);   // => condition_mean ~ normal(overall_mean, condition_mean_sd)
+    for (i in 1:n) {
+      response[i] ~ normal(condition_mean[condition[i]], response_sd);
+    }
+  }
+')
+```
+
+
+```{stan ABC_stan_model, output.var = "ABC_stan", results = "hide", eval = FALSE}
 data {
   int<lower=1> n;
   int<lower=1> n_condition;
@@ -629,7 +670,7 @@ bayes_results
 
 Here, `to_broom_names()` will convert `.lower` and `.upper` into `conf.low` and `conf.high` so the names of the columns we need to make the comparison (`condition`, `estimate`, `conf.low`, and `conf.high`) all line up easily. This makes it simple to combine the two tidy data frames together using `bind_rows`, and plot them:
 
-```{r fig.width = tiny_width, fig.height = tiny_height}
+```{r fig.width = tiny_width, fig.height = tiny_height, eval = eval_chunks && requireNamespace("emmeans", quietly = TRUE)}
 bind_rows(linear_results, bayes_results) %>%
   mutate(condition = fct_rev(condition)) %>%
   ggplot(aes(y = condition, x = estimate, xmin = conf.low, xmax = conf.high, color = model)) +