Instructions for compiling manuscripts

Install dependencies

Install the dependencies required for the supplementary examples using the devtools package:

install.packages("devtools")
devtools::install_github(c("egonw/rrdf/rrdflibs", "egonw/rrdf/rrdf", "cboettig/Sxslt"))

Then install the RNeXML R package, including the suggested packages, using the following R command:

install.packages("RNeXML", dependencies=TRUE)

Note that rmarkdown requires pandoc (>= 0.12.3) and pandoc-citeproc be installed. These ship with the current version of RStudio (>=0.98). Additionally, a LaTeX environment is required to generate the output pdf.

Build the manuscript

Make sure you set the manuscripts/ as your working directory and then do:

rmarkdown::render("manuscript.Rmd")

or use the knit2pdf button in your RStudio console.

Alternately: Using Docker

Instead of installing R packages seperately, you can try out RNeXML by running RStudio in a Docker container. This (a) avoids having to install software dependencies, and (b) avoids altering anything on your local library. If the above doesn't work, or just for fun, give this a try.

The RNeXML package and all dependencies are installed on the rocker/ropensci⁠ Docker container. You will still need all the files from this directory (the manuscripts directory on the RNeXML Github repository) to build the manuscript. Users can decide to run either an R console (accessed through a terminal) or an RStudio instance (accessed through the browser) on the container.

Docker Installation

In a Mac or Windows machine, this will aslo install boot2docker (easy point & click install, ~24 MB). On Linux, this installs natively and we can run everything in the terminal instead of in the boot2docker window. ([Mac⁠], [Windows⁠, [Linux⁠]).

R console

With boot2docker running, run R on the rocker/ropensci image, linking the location of your copy of this directory to /home/rstudio on the container, setting the container's working directory to the same, and setting user as rstudio:

docker run -v /path/to/RNeXML/manuscripts:/home/rstudio \ 
  -w /home/rstudio -u rstudio -ti --rm rocker/ropensci R

At the R prompt, you can use rmarkdown to render the manuscript PDF from the Rmd file:

rmarkdown::render('manuscript.Rmd')

manuscript.pdf should now be created in the manuscripts directory.

Using RStudio

1. From the command line (with boot2docker running on Mac/Windows), do:

sudo docker run -d -p 8787:8787 rocker/ropensci

That will take a while to download the image the first time you run it.

1. Once it is done, try:

boot2docker ip

that should return an ip address you can paste into your browser.

1. Add a :8787 to the end of this address and paste it into your browser address bar. (e.g. it's probably http://92.168.59.103:8787 but that can change).

2. You should get the RStudio welcome screen. you should be able to login with user/password rstudio/rstudio.

3. Clone the RNeXML repository using New Project from Version Control (https://github.com/ropensci/RNeXML⁠), switch into the manuscripts directory and you should be good to go as above.