title: Highlighting bash code with knitr / rmarkdown
body: <p>I'm trying to generate an HTML report using RStudio, R Markdown and knitr. In the report I would like to display some <code>bash</code> code. I do not want to run the code but I would like it to be highlighted.</p>
  
  <p>It has been mentioned in <a href="https://stackoverflow.com/a/29223248/3017012">another question</a> but the suggestion there doesn't work for me. Here's what I've tried so far:</p>
  
  <pre><code>---
  title: "bash highlighting?"
  output: html_document
  ---
  ```{r, engine = 'bash', eval = FALSE}
  for foo in (ls bar)
  do
    echo $foo
  done
  ```
  
  ```{bash, eval = FALSE}
  for foo in (ls bar)
  do
    echo $foo
  done
  ```
  </code></pre>
  
  <p>Neither of these give me highlighting in the HTML document. I know it's possible because I remember seeing it somewhere a week or so ago, but I can't find it anymore! Does anyone know how I can achieve it?</p>
  
  <p>Thanks for reading,</p>
  
  <p>Tom</p>
  
  <p>Edit: I just found <a href="https://stackoverflow.com/a/14697524/3017012">this answer</a>, which suggests using the following code block in the .Rmd</p>
  
  <pre><code>&lt;link rel="stylesheet" href="http://yandex.st/highlightjs/7.3/styles/default.min.css"&gt;
  &lt;script src="http://ajax.googleapis.com/ajax/libs/jquery/1.9.0/jquery.min.js"&gt;&lt;/script&gt;
  &lt;script src="http://yandex.st/highlightjs/7.3/highlight.min.js"&gt;&lt;/script&gt;
  &lt;script&gt;
  $(document).ready(function() {
    $('pre code').each(function(i, e) {hljs.highlightBlock(e)});
  });
  &lt;/script&gt;
  </code></pre>
  
  <p>This works for the bash code in the document but kills the highlighting for the R code!</p>
  
  <pre><code>## R version 3.2.0 (2015-04-16)
  ## Platform: x86_64-pc-linux-gnu (64-bit)
  ## Running under: Ubuntu 14.04.2 LTS
  ## 
  ## locale:
  ##  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
  ##  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
  ##  [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
  ##  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
  ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
  ## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
  ## 
  ## attached base packages:
  ## [1] stats     graphics  grDevices utils     datasets  methods   base     
  ## 
  ## loaded via a namespace (and not attached):
  ## [1] formatR_1.2     tools_3.2.0     htmltools_0.2.6 yaml_2.1.13    
  ## [5] rmarkdown_0.5.1 knitr_1.10      stringr_0.6.2   digest_0.6.8   
  ## [9] evaluate_0.7
  </code></pre>