knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
A recent version of Pandoc (>= 1.12.3) is required to use the rmarkdown package. RStudio also automatically includes this so you do not need to download Pandoc if you plan to use rmarkdown from the RStudio IDE.
If not using the RStudio IDE, you'll need to install Pandoc for your platform.
Windows and Mac OS X
The pandoc installation page includes easy to use installers for Windows and Mac OS X.
The version of pandoc included in the standard repositories is not recent enough for use with the rmarkdown package. You can install a more recent version of pandoc by installing the Haskell Platform and then following these instructions for building pandoc from source.
This method installs a large number of Haskell dependencies so might not be desirable. You can also obtain a standalone version of pandoc without the dependencies as follows:
Older Systems (RHEL 5)
For older Linux systems you can obtain a standalone version of pandoc v1.13.1 (with no Haskell dependencies) from https://copr.fedoraproject.org/coprs/petersen/pandoc-el5/ as follows:
$ sudo wget -P /etc/yum.repos.d/ https://copr.fedoraproject.org/coprs/petersen/pandoc-el5/repo/epel-5/petersen-pandoc-el5-epel-5.repo $ yum install pandoc pandoc-citeproc
Newer Systems (Debian/Ubuntu/Fedora/RHEL6+)
For newer Linux systems you can make a standalone version of pandoc v1.12.3 available to the system by soft-linking the binaries included with RStudio:
$ sudo ln -s /usr/lib/rstudio/bin/pandoc/pandoc /usr/local/bin $ sudo ln -s /usr/lib/rstudio/bin/pandoc/pandoc-citeproc /usr/local/bin
If you are running RStudio Server the commands would be:
$ sudo ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc /usr/local/bin $ sudo ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc /usr/local/bin
If you aren't running RStudio at all you can simply copy the binaries out of the RStudio
bin/pandoc directory and locate them within
/usr/local/bin on your target system.