Why does RStudio show the manually knitted pdf wro

I'm running the latest RStudio (0.97.551) and R (3.0.1) version on Mac OS X Mountain Lion 10.8.4.

I have the following two files: test.Rnw

\documentclass{article}

<<set-options, echo=FALSE>>=
 options(replace.assign=TRUE)
 opts_chunk$set(external=TRUE, cache=TRUE, echo=FALSE, fig=TRUE)
 read_chunk('chunks.R')
@

\begin{document}
\section{Graphics}

<<chart, fig.height=4>>=
@

\end{document}

and chunks.R

## @knitr chart
library(ggplot2, quietly=TRUE)
Sys.sleep(3)
p <- ggplot(mtcars, aes(wt, mpg))  + geom_point(aes(size = qsec)) +
   labs(title ="title with umlauts ä")
p
sessionInfo()

When knitting this document in RStudio everything is fine:

Now I clear the cache and knit the document manually from a script running the commands:

export TEXINPUTS=$TEXINPUTS:/Library/Frameworks/R.framework/Versions/Current/Resources/share/texmf/tex/latex/
/usr/bin/Rscript -e "library(knitr); knit(\"test.Rnw\")"
pdflatex ./test.tex

Everything is still fine.

But then I don't clear the cache and knit again in RStudio. the PDF-viewer of RStudio now displays the chart as follows:

Mac OS X Preview shows both pdfs fine. The only difference in sessionInfo() I can see is the order of the base packages.

Has anyone an idea why RStudio shows the graphic wrong?

I don't know how to share the two pdfs. So if anyone needs them and tells me how to share them, I'll do it.

TIA, JW

RStudio sets grDevices::pdf.options(useDingbats = FALSE) before it calls knitr (see the panel Compile PDF which contains the log), and the option useDingbats is TRUE by default in R. RStudio's built-in PDF viewer does not honor the Dingbats font, so the circles (solid points) were broken in its PDF viewer when useDingbats = TRUE. See ?pdf for more information.

You should not use RStudio's PDF viewer to view the PDF generated outside of RStudio by yourself. There are other good choices in Tools -> Options -> Sweave -> PDF preview, such as Sumutra PDF under Windows, and evince under Linux. I have no idea about Mac OS X, though (at least you can use the default viewer of the system, I believe).