Merge pull request #1222 from stan-dev/fix-compile-example

cleanly handle compiling with threads in compile doc

Author: jgabry

R/model.R

@@ -533,17 +533,23 @@ NULL
 #'
 #' @examples
 #' \dontrun{
-#' file <- file.path(cmdstan_path(), "examples/bernoulli/bernoulli.stan")
+#' stan_file <- file.path(cmdstan_path(), "examples/bernoulli/bernoulli.stan")
 #'
 #' # by default compilation happens when cmdstan_model() is called.
 #' # to delay compilation until calling the $compile() method set compile=FALSE
-#' mod <- cmdstan_model(file, compile = FALSE)
+#' mod <- cmdstan_model(stan_file, compile = FALSE)
 #' mod$compile()
 #' mod$exe_file()
 #'
-#' # turn on threading support (for using functions that support within-chain parallelization)
-#' mod$compile(force_recompile = TRUE, cpp_options = list(stan_threads = TRUE))
-#' mod$exe_file()
+#' # turn on threading support for using functions that support within-chain
+#' # parallelization or running multiple pathfinder paths in parallel
+#' # (here we compile a copy of the model in a temporary directory so that the
+#' # executable compiled without threading above is not overwritten)
+#' stan_file_threads <- file.path(tempdir(), "bernoulli.stan")
+#' file.copy(stan_file, stan_file_threads)
+#' mod_threads <- cmdstan_model(stan_file_threads, compile = FALSE)
+#' mod_threads$compile(cpp_options = list(stan_threads = TRUE))
+#' mod_threads$cpp_options()
 #'
 #' # turn on pedantic mode
 #' file_pedantic <- write_stan_file("
@@ -554,8 +560,9 @@ NULL
 #'   sigma ~ exponential(1);
 #' }
 #' ")
-#' mod <- cmdstan_model(file_pedantic, pedantic = TRUE)
-#'
+#' mod <- cmdstan_model(file_pedantic, compile = FALSE)
+#' mod$compile(pedantic = TRUE)
+#' # same as mod <- cmdstan_model(file_pedantic, pedantic = TRUE)
 #' }
 #'
 compile <- function(quiet = TRUE,