Add hook so that output from R Markdown chunks which generate a warning

or an error has the class "error" and appears in red font.

https://github.com/swcarpentry/lesson-example/blob/gh-pages/LAYOUT.md#topics

tools/chunk-options.R

@@ -9,7 +9,7 @@ opts_chunk$set(tidy = FALSE, results = "markup", comment = NA,
                fig.align = "center", fig.path = "fig/")
 
 # The hooks below add html tags to the code chunks and their output so that they
-# are properly formatted when the site is built with jekyll.
+# are properly formatted when the site is built.
 hook_in <- function(x, options) {
   stringr::str_c("\n\n~~~{.r}\n",
                  paste0(x, collapse="\n"),
@@ -22,5 +22,11 @@ hook_out <- function(x, options) {
                  "\n~~~\n\n")
 }
 
-knit_hooks$set(source = hook_in, output = hook_out, warning = hook_out,
-               error = hook_out, message = hook_out)
+hook_error <- function(x, options) {
+  stringr::str_c("\n\n~~~{.error}\n",
+                 paste0(x, collapse="\n"),
+                 "\n~~~\n\n")
+}
+
+knit_hooks$set(source = hook_in, output = hook_out, warning = hook_error,
+               error = hook_error, message = hook_out)