R Markdown and Animation - Animated Plot Cuts Trail of Document

[s-fiebig]

Using R Markdown to include animations cuts all content after the animation.

First of all, I'm not entirely sure if the fault is with knitr or another part of the R Markdown Toolchain, but as I've solved it temporarily in knitr, I'm posting here.

OSX
R Version 3.2.1
knitr 1.10.5
R Markdown 0.7

Using the sample from the knitr docu about animation or from stackexchange (http://stackoverflow.com/questions/12038893/combining-r-markdown-and-animation-package) with additional content results in a html with all content missing after the animated plot. E.g.:

```{r clock, fig.width=7, fig.height=6, fig.show='animate'}
par(mar = rep(3, 4))
for (i in seq(pi/2, -4/3 * pi, length = 12)) {
    plot(0, 0, pch = 20, ann = FALSE, axes = FALSE)
    arrows(0, 0, cos(i), sin(i))
    axis(1, 0, "VI"); axis(2, 0, "IX")
    axis(3, 0, "XII"); axis(4, 0, "III"); box()
}
```
Everything from here on is missing.

Reason is the wrong html that is created:

...
<source src="bob" /><p>video of chunk clock</video></p>
...

The video and p tag are disordered. I haven't found (didn't look extensively) the code part introducing the paragraph tags and solved it by adding p tags myself in

knitr/R/hooks-html.R

Line 90 in fda7825

sprintf('<video %s><source src="%s" />video of chunk %s</video>',

sprintf('<video %s><source src="%s" /><p>video of chunk %s</p></video>',

[yihui]

Thanks for the report. I can reproduce it. I think it is a Pandoc issue. Here is a minimal repro:

test.md

<video ><source src="foo"/>asdf</video>

Run pandoc test.md -o test.html and you get:

<video >
<source src="foo"/>
<p>asdf</video></p>

I have verified that the current latest version of Pandoc (1.15.0.4) still has the problem. I guess you can move it to https://github.com/jgm/pandoc/issues

[s-fiebig]

Thanks for checking this! Will move the issue (jgm/pandoc#2290).

[s-fiebig]

jgm did "not" accept this as a bug for the time being. He suggested introducing a paragraph (jgm/pandoc#2290), what is as good as writing the p tags (what I did).
I'm leaving the decision to you and don't do a pull request, unless told otherwise.
You can close the issue at your discretion.

[yihui]

Thanks a lot! A simple pull request adding <p></p> will be welcome :)

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