New Wine in an Old Bottle: R Markdown v2 and R Studio on the Cent OS Server

• Introduction
• New Pandoc
• Installing LaTeX Packages

Introduction

R Markdown Version 2 is a boon to students: with a single click one can convert an R Markdown file to either HTML, PDF or Word format. However, getting this feature to work fully in the R Studio server environment may require a bit of work, especially if you running the Server on a Cent OS distribution. Although I am sure that Cent OS has many virtues, an up-to-date repository is not among them.

This post is the record of an arm wrasslin’ match with Cent OS and the R Studio Server version 0.98.932, from which I emerged more or less victorious. If your IT department hosts RStudio on CentOS, then perhaps the following remarks will make your life a bit easier. On the other hand, if you know your way around Linux better than I do, please feel free to offer quicker or better solutions in the Comments.

Log on to the server, perhaps through ssh (secure shell). Come armed with administrative privileges.

New Pandoc

R Markdown v2 uses a newer version of the pandocconverter than the one available in the Cent OS repository. Fortunately, R Studio comes bundled with the binaries of a sufficiently recent version of pandoc. You obtain access to these files by establishing symbolic links in the /usr/local/bin directory to the pandoc and pandoc-cite binaries:

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sudo ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc /usr/local/bin
sudo ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc /usr/local/bin

Installing LaTeX Packages

You can get Tex Live from the Cent OS repositories, but the release appears to date back to the year 2007. Therefore it lacks a couple of packages needed by pandoc:

• Heiko Oberdiek’s ifluatex, and
• Donald Arsenau’s framed.

Since you will download these packages from the Comprehensive Tex Archive Network, you’ll want a web-fetch utility such as wget. If it’s not already installed on Cent OS, you can get it with:

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sudo yum install wget

Now you can grab the relevant files with wget:

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wget http://www.ctan.org/tex-archive/macros/latex/contrib/oberdiek/ifluatex.dtx
wget http://mirrors.ctan.org/macros/latex/contrib/framed.zip

Turning first to ifluatex, we begin by by unpacking the .dtx bundle. This is accomplished with a tex command:

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tex ifluatex.dtx

Several files spill out into your Home directory. You care only about ifluatex.sty. Copy it as follows:

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sudo cp ifluatex.sty /usr/share/texmf/tex/generic/oberdiek

As for the framed package, you must first unzip the downloaded file into a directory:

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mkdir framed
unzip framed.zip -d framed

Now copy the framed directory as follows:

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sudo cp -rf framed /usr/share/texmf/tex/latex

Finally, you need to make tex aware of the existence of these new packages with texhash:

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sudo texhash

Now you may Knit to your heart’s content!