New Wine in an Old Bottle: R Markdown v2 and R Studio on the Cent OS Server28 Aug 2014
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.
R Markdown v2 uses a newer version of the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
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
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:
sudo yum install wget
Now you can grab the relevant files with
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
Several files spill out into your Home directory. You care only about
ifluatex.sty. Copy it as follows:
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:
mkdir framed unzip framed.zip -d framed
Now copy the
framed directory as follows:
sudo cp -rf framed /usr/share/texmf/tex/latex
Finally, you need to make tex aware of the existence of these new packages with
Now you may Knit to your heart’s content!