The self-contained mode can mangle JavaScript in Markdown

[yihui]

Here is a minimal test case test.md:

hello world!

<script type="text/javascript">
var pow = 1.2, value=5;
while (pow<value) {
pow *= 2;
}
</script>

I convert it to HTML using Pandoc 1.12.3:

pandoc test.md -o test.html --self-contained

And I get the HTML output:

....
<p>hello world!</p>
<script type="text/javascript">
var pow = 1.2, value=5;
while (pow<value) { pow *="2;" } < script>
</body>
....

There are two problems in the conversion:

1. pow *= 2; becomes pow *="2;", which is invalid in JavaScript;
2. </script> becomes < script> (/ was removed for some reason).

[yihui]

Thanks for the hint! Here is a full example: http://stackoverflow.com/q/23021317/559676 I had to turn off the --self-contained option to preserve the JavaScript code.

According to the documentation, the text between <script> and </script> should not be affected by the extension markdown_in_html_blocks:

There is one exception to this rule: text between <script> and <style> tags is not interpreted as markdown.

[Thell]

Sorry about the @yihui, my bad re: markdown_in_html_blocks, I had removed it after realizing that I couldn't reproduce the problem either from the command line or via RStudio. FWIW, I also can't reproduce a problem with the full example you just posted either via RStudio Version 0.98.760 with supplied pandoc using render(), or knit/pandoc or from the command line with pandoc; the only issue is a font warning from open3d().

[Edit] - I forgot I had linked the RStudio pandoc to ~/.cabal/bin/pandoc which is version 1.12.3.3!! After switching it back, a message that javascript was required was on the page, but only when using render() from rstudio, not with knit/pandoc or pandoc from the commandline.

[jgm]

This is a bug in tagsoup 0.13 which has been fixed in tagsoup 0.13.1:
https://hackage.haskell.org/package/tagsoup-0.13.1/changelog

I can confirm that the problem goes away if you compile against tagsoup 0.13.1:

cabal install pandoc --constrain 'tagsoup==0.13.1'

[yihui]

Perfect. Thanks!