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POWhy does RStudio show the manually knitted pdf wrong?
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  1. POWhy does RStudio show the manually knitted pdf wrong?
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    copied!<p>I'm running the latest RStudio (0.97.551) and R (3.0.1) version on Mac OS X Mountain Lion 10.8.4.</p> <p>I have the following two files: test.Rnw</p> <pre><code>\documentclass{article} &lt;&lt;set-options, echo=FALSE&gt;&gt;= options(replace.assign=TRUE) opts_chunk$set(external=TRUE, cache=TRUE, echo=FALSE, fig=TRUE) read_chunk('chunks.R') @ \begin{document} \section{Graphics} &lt;&lt;chart, fig.height=4&gt;&gt;= @ \end{document} </code></pre> <p>and chunks.R</p> <pre><code>## @knitr chart library(ggplot2, quietly=TRUE) Sys.sleep(3) p &lt;- ggplot(mtcars, aes(wt, mpg)) + geom_point(aes(size = qsec)) + labs(title ="title with umlauts ä") p sessionInfo() </code></pre> <p>When knitting this document in RStudio everything is fine:</p> <p><img src="https://i.stack.imgur.com/VQonm.png" alt="generated with RStudio"></p> <p>Now I clear the cache and knit the document manually from a script running the commands:</p> <pre><code>export TEXINPUTS=$TEXINPUTS:/Library/Frameworks/R.framework/Versions/Current/Resources/share/texmf/tex/latex/ /usr/bin/Rscript -e "library(knitr); knit(\"test.Rnw\")" pdflatex ./test.tex </code></pre> <p>Everything is still fine.</p> <p>But then I don't clear the cache and knit again in RStudio. the PDF-viewer of RStudio now displays the chart as follows:</p> <p><img src="https://i.stack.imgur.com/MInty.png" alt="Regenerated with RStudio after chunks are generated manually"></p> <p>Mac OS X Preview shows both pdfs fine. The only difference in sessionInfo() I can see is the order of the base packages.</p> <p>Has anyone an idea why RStudio shows the graphic wrong?</p> <p>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.</p> <p>TIA, JW</p>
 

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