From 386aa21b57c6d0709f636988d5074482224b18cb Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Sun, 1 Oct 2023 17:35:47 +0300
Subject: [PATCH 1/2] Add dedicated hpp generation step

---
 R/model.R |  7 ++++---
 R/utils.R | 10 +++++-----
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/R/model.R b/R/model.R
index c8d6ea60..3031aed9 100644
--- a/R/model.R
+++ b/R/model.R
@@ -626,10 +626,13 @@ compile <- function(quiet = TRUE,
   }
   stancflags_standalone <- c("--standalone-functions", stancflags_val, stancflags_combined)
   self$functions$hpp_code <- get_standalone_hpp(temp_stan_file, stancflags_standalone)
+  private$model_methods_env_ <- new.env()
+  private$model_methods_env_$hpp_code_ <- get_standalone_hpp(temp_stan_file, c(stancflags_val, stancflags_combined))
   self$functions$external <- !is.null(user_header)
   self$functions$existing_exe <- FALSE
 
-  stancflags_val <- paste0("STANCFLAGS += ", stancflags_val, paste0(" ", stancflags_combined, collapse = " "))
+  all_stancflags <- paste0(stancflags_val, paste0(" ", stancflags_combined, collapse = " "))
+  stancflags_val <- paste0("STANCFLAGS += ", all_stancflags)
 
   if (!dry_run) {
 
@@ -712,10 +715,8 @@ compile <- function(quiet = TRUE,
   private$precompile_cpp_options_ <- NULL
   private$precompile_stanc_options_ <- NULL
   private$precompile_include_paths_ <- NULL
-  private$model_methods_env_ <- new.env()
 
   if(!dry_run) {
-    suppressWarnings(private$model_methods_env_$hpp_code_ <- readLines(private$hpp_file_, warn = FALSE))
     if (compile_model_methods) {
       expose_model_methods(env = private$model_methods_env_,
                             verbose = !quiet,
diff --git a/R/utils.R b/R/utils.R
index 4f40ca0c..be03344b 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -800,6 +800,10 @@ create_skeleton <- function(param_metadata, model_variables,
 }
 
 get_standalone_hpp <- function(stan_file, stancflags) {
+  name <- strip_ext(basename(stan_file))
+  path <- dirname(stan_file)
+  hpp_path <- file.path(path, paste0(name, ".hpp"))
+
   status <- withr::with_path(
       c(
         toolchain_PATH_env_var(),
@@ -807,16 +811,12 @@ get_standalone_hpp <- function(stan_file, stancflags) {
       ),
       wsl_compatible_run(
         command = stanc_cmd(),
-        args = c(stan_file,
-                stancflags),
+        args = c(paste0("--o=", hpp_path), stancflags, stan_file),
         wd = cmdstan_path(),
         error_on_status = FALSE
       )
     )
   if (status$status == 0) {
-    name <- strip_ext(basename(stan_file))
-    path <- dirname(stan_file)
-    hpp_path <- file.path(path, paste0(name, ".hpp"))
     hpp <- suppressWarnings(readLines(hpp_path, warn = FALSE))
     unlink(hpp_path)
     hpp

From d180e4e275a58f315aca687aa32474ce2e266d2a Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Sun, 1 Oct 2023 17:39:14 +0300
Subject: [PATCH 2/2] Stray change

---
 R/model.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/model.R b/R/model.R
index 3031aed9..c061e9ac 100644
--- a/R/model.R
+++ b/R/model.R
@@ -631,8 +631,7 @@ compile <- function(quiet = TRUE,
   self$functions$external <- !is.null(user_header)
   self$functions$existing_exe <- FALSE
 
-  all_stancflags <- paste0(stancflags_val, paste0(" ", stancflags_combined, collapse = " "))
-  stancflags_val <- paste0("STANCFLAGS += ", all_stancflags)
+  stancflags_val <- paste0("STANCFLAGS += ", stancflags_val, paste0(" ", stancflags_combined, collapse = " "))
 
   if (!dry_run) {