What's worse, if RStudio is uninstalled and then re-installed to fix the order, the problem remains. But, if the installation order is reversed, the LaTeX engine crashes (this happens pdflatex.exe, lulatex.exe, and xelatex.exe). On two separate Windows machines (both running Windows 7 Enterprise) I've found that if MiKTeX is installed before RStudio I can create pdf output without problem. Note: this request has also been made on the RStudio Support site
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