HTML output of Stan chunks can be malformed

[bgoodri]

With RStudio >= 1.0, when knitting a RMarkdown file to HTML, a chunk with Stan code can render improperly unless extra spacing is included.

For example, this chunk

```{stan output.var="test", eval = FALSE}
parameters {real < lower = 0 > theta;}
model {target += exponential_lpdf(theta | 1);}
```

looks okay when knit to HTML.

However, without the extra space before and after the angle brackets, as in

```{stan output.var="test", eval = FALSE}
parameters {real<lower = 0> theta;}
model {target += exponential_lpdf(theta | 1);}
```

the HTML file omits the <.

Similarly, without the extra spaces before and after the equal sign, as in

```{stan output.var="test", eval = FALSE}
parameters {real < lower=0 > theta;}
model {target += exponential_lpdf(theta | 1);}
```

the HTML omits the first =.

If you knit to PDF, none of these problems occur, so I think it is probably as issue that < and > need to be interpreted literally in the HTML. The Stan language is whitespace insensitive, so it is a bit odd to have to add extra whitespace to get decent HTML output.

[jjallaire]

@yihui Any idea why this might be the case?

[jmcphers]

FWIW I was able to repro this trivially (had rmarkdown 1.2.9000 and knitr 1.15.1 locally). I wonder if it's actually a bug in the highlighter as the output from knitr looks fine prior to the highlight pass (HTML entities properly escaped):

<pre class="stan"><code>parameters {real &lt;lower = 0&gt; theta;}
model {target += exponential_lpdf(theta | 1);}</code></pre>

[yihui]

I just tested it, and I think it is a highlight.js bug. We are still using 1.1, and the official version is 9.8.0 now: https://highlightjs.org/ I tested 9.8.0 and it works fine.

[jjallaire]

We could test this by changing the highligher to one of the pandoc based ones (the "default" and "textmate" highlighters use highlight.js, the other highlighters use pandoc)

…

On Tue, Dec 13, 2016 at 4:50 PM, Jonathan ***@***.***> wrote: FWIW I was able to repro this trivially (had rmarkdown 1.2.9000 and knitr 1.15.1 locally). I wonder if it's actually a bug in the highlighter as the output from knitr looks fine prior to the highlight pass (HTML entities properly escaped): <pre class="stan"><code>parameters {real &lt;lower = 0&gt; theta;} model {target += exponential_lpdf(theta | 1);}</code></pre> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#907 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAGXx60f-9rwYrL1-jCQYEkIXPCuJeiHks5rHxMVgaJpZM4LMNQU> .

[jjallaire]

For now I'd say the workaround is to change the highlighter to "tango", "pygments", "kate", "monochrome", "espresso", "zenburn", or "haddock"

[yihui]

Duplicate of #988.

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