Highlighting bash code with knitr / rmarkdown

Question

I\'m trying to generate an HTML report using RStudio, R Markdown and knitr. In the report I would like to display some bash code. I do not want to run the code

Answer 1

The default syntax highlighting theme does not work well for non-R code chunks, and you can use other themes, e.g. pygments

---
title: "Bash Highlighting"
output:
  html_document:
    highlight: pygments
---

```{r, engine = 'bash', eval = FALSE}
for foo in (ls bar)
do
  echo $foo
done
```

Answer 2

OK, figured it out thanks to the comments. It seems it's RStudio which is not playing nice with the highlighting. When I keep the intermediate markdown file as in.md:

---
title: "Bash Highlighting"
output:
  html_document:
    keep_md: true
---

```{r, engine = 'bash', eval = FALSE}
for foo in (ls bar)
do
  echo $foo
done
```

then convert to html with pandoc using e.g. the CSS from BioConductor:

pandoc -s in.md \
    -c https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/BiocStyle/inst/resources/html/bioconductor.css \
    -t html -o out.html

I get nice code highlighting for R and bash.

Thanks!