From adebd6a794f0f95fb48e89a8c64bda3cf90ede9b Mon Sep 17 00:00:00 2001
From: jgabry <jgabry@gmail.com>
Date: Thu, 17 Dec 2020 10:38:20 -0700
Subject: [PATCH] fix r cmd check NOTE about assignment to global env

the idea for this fix comes from https://github.com/yihui/knitr/issues/1824#issuecomment-647333232
---
 R/knitr.R |  2 +-
 R/zzz.R   | 29 ++++++++++++++++++++---------
 2 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/R/knitr.R b/R/knitr.R
index 201374e1e..21c4fc55e 100644
--- a/R/knitr.R
+++ b/R/knitr.R
@@ -80,7 +80,7 @@ eng_cmdstan <- function(options) {
     }
     file <- write_stan_file(options$code, dir = dir)
     mod <- cmdstan_model(file)
-    assign(output_var, mod, envir = knitr::knit_global())
+    assign(output_var, mod, envir = cmdstanr_knitr_env())
   }
   options$engine <- "stan" # for syntax highlighting
   code <- paste(options$code, collapse = "\n")
diff --git a/R/zzz.R b/R/zzz.R
index a656a2eb4..6147d4f2d 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,12 +1,3 @@
-.onAttach <- function(...) {
-  startup_messages()
-}
-
-.onLoad <- function(...) {
-  cmdstanr_initialize()
-}
-
-
 startup_messages <- function() {
   packageStartupMessage("This is cmdstanr version ", utils::packageVersion("cmdstanr"))
   packageStartupMessage("- Online documentation and vignettes at mc-stan.org/cmdstanr")
@@ -65,3 +56,23 @@ cmdstanr_initialize <- function() {
   }
   invisible(TRUE)
 }
+
+cmdstanr_knitr_env_function_generator <- function(env1) {
+  function(env2 = NULL) {
+    if (!is.null(env2)) {
+      env1 <<- env2
+    }
+    invisible(env1)
+  }
+}
+cmdstanr_knitr_env <- cmdstanr_knitr_env_function_generator(new.env())
+
+
+.onAttach <- function(...) {
+  startup_messages()
+}
+
+.onLoad <- function(...) {
+  cmdstanr_knitr_env(knitr::knit_global())
+  cmdstanr_initialize()
+}