Bootstrap alerts in R Markdown

The default errors, warnings and messages in R Markdown are OK, but HTML output could look so much better in HTML, considering the templates use Twitter Bootstrap by default.

Let’s see what we can do instead with a few CSS classes!

stop('This should break!')

Error in eval(expr, envir, enclos): This should break!

warning('Watch out!')

Warning Watch out!

message('This is a message for you')

This is a message for you

All this was achieved with the following knitr settings. Potentially, LaTeX templates could be written for PDF and Beamer output as well.

knitr::knit_hooks$set(
   error = function(x, options) {
     paste('\n\n<div class="alert alert-danger">',
           gsub('##', '\n', gsub('^##\ Error', '**Error**', x)),
           '</div>', sep = '\n')
   },
   warning = function(x, options) {
     paste('\n\n<div class="alert alert-warning">',
           gsub('##', '\n', gsub('^##\ Warning:', '**Warning**', x)),
           '</div>', sep = '\n')
   },
   message = function(x, options) {
     paste('\n\n<div class="alert alert-info">',
           gsub('##', '\n', x),
           '</div>', sep = '\n')
   }
)

Notice the regular expressions, which replace the ## Error/## Warning with bold text. (It is necessary to get rid of the hashes to avoid the text being turned into a level two (<h2>) header, but you could also adjust the comment chunk option.) Is there a way of accessing the errors/warnings/messages before this stage for a more elegant solution?

What if the messages go onto multiple lines? The double gsub should take care of it.

stop('This\nshould\nbreak!\n')

Error in eval(expr, envir, enclos): This

should

break!

warning('Watch\nout!')

Warning Watch

out!

message('Let\nthat\nbe\na\nmessage')

Let

that

be

a

message

A better solution, perhaps, might be to read carefully what is written at https://yihui.name/knitr/hooks/ and consider the knitr::render_html() function. Doing things this way might also side-step the problem of writing conditional markup for the different output formats.

After a bit of research, the solution to the multi-line commenting problem appears to lie in the functions knitr:::wrap.error, wrap.message and wrap.warning. My idea is: just trick them into thinking that options$comment has been set to an empty string, and leave everything else the same.

wrap.error <- function(x, options) {
  options$comment <- ""
  knitr:::msg_wrap(paste(x$message, collapse = ""), "error", options)
}
wrap.message <- function(x, options) {
  options$comment <- ""
  knitr:::msg_wrap(paste(x$message, collapse = ""), "message", options)
}
wrap.warning <- function(x, options) {
  options$comment <- ""
  knitr:::msg_wrap(paste(x$message, collapse = ""), "warning", options)
}

But it is not easy, as far as I can tell, to replace non-exported S3 functions in packages, so short of forking the entire knitr package and rebuilding it with this file changed, the find-and-replace strategy will have to do.