.swf created by knitr and hook_r2swf overlapping - r

Question

I try to make a dynamic presentation with knitr and animation. I pick the hook_r2swf which is the only one works on my machine.
For example, I knit the following .Rmd files:
# Test Animation
```{r, fig.show='animate', aniopts='autoresume'}
opts_knit$set(animation.fun = hook_r2swf)
plot(1,1,type="n")
plot(2,2,type='n')
```
However, it seems that the .swf will overlap all figures plotted in the chunk which may look like this:
<p><embed width="504" height="504" name="plugin" src="https://dl.dropbox.com/u/11900271/unnamed-chunk-1.swf" type="application/x-shockwave-flash"></p>
Does anyone know how to make the result non-overlapping?
I am using ubuntu 12.04 with following session info:
R version 2.15.3 (2013-03-01)
Platform: i686-pc-linux-gnu (32-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] testpkg_1.0 xts_0.9-1 zoo_1.7-9 Rcpp_0.10.2 roxygen2_2.2.2 digest_0.5.2
[7] knitr_1.1
loaded via a namespace (and not attached):
[1] brew_1.0-6 evaluate_0.4.3 formatR_0.6 grid_2.15.3 lattice_0.20-13 stringr_0.6.2
[7] tools_2.15.3
Thanks!

Answer 1

This seems to be an issue in the way animation is handled. The two plots are placed on top of each other. While I am not sure exactly how to prevent that itself, I can suggest the following workaround. By default, the background is transparent. If we change the background to white, the problem is solved:
```{r, fig.show='animate'}
opts_knit$set(animation.fun = hook_r2swf)
par(bg="white")
plot(1,1,type="n")
plot(2,2,type='n')
```