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Setting Up the Development Version of R

John Ramey

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My coworkers at Fred Hutchinson regularly use the development version of R (i.e., R-devel) and have urged me to do the same. This post details how I have set up the development version of R on our Linux server, which I use remotely because it is much faster than my Mac.

First, I downloaded the R-devel source into ~/local/, which is short for /home/jramey/local/ via Subversion, configured my installation, and compiled the source. I recommend these Subversion tips if you are building from source. Here are the commands to install R-devel.

bash svn co https://svn.r-project.org/R/trunk ~/local/R-devel cd ~/local/R-devel ./tools/rsync-recommended ./configure --prefix=/home/jramey/local/ make make install

The third command downloads the recommended R packages and is crucial because the source for the recommended R packages is not included in the SVN repository. For more about this, go here.

We have the release version (currently, it is 2.15.1) installed in /usr/local/bin. But the goal here is to give priority to R-devel. So, I add the following to my ~/.bashrc file:

“` bash PATH=~/local/bin:$PATH export PATH

Never save or restore when running R

alias R=’R –no-save –no-restore-data –quiet’ “`

Notice that the last line that I add to my ~/.bashrc file is to load R-devel quietly without saving or restoring.

Next, I install the R packages that I use the most.

r install.packages(c('devtools', 'ProjectTemplate', 'knitr', 'ggplot2', 'reshape2', 'plyr', 'Rcpp', 'mvtnorm', 'caret'), dep = TRUE)

Then, I update my .Rprofile file, which I keep in a Github gist.

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          <dt>t</dt>
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          <dt>e <em>or</em> shift i <em>or</em> y</dt>
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          <dt>shift m</dt>
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      <h3>Format Text</h3>
      <p>Headers</p>
      <pre>
# This is an &lt;h1&gt; tag
## This is an &lt;h2&gt; tag
###### This is an &lt;h6&gt; tag</pre>
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     <pre>
*This text will be italic*
_This will also be italic_
**This text will be bold**
__This will also be bold__

*You **can** combine them*
</pre>
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      <h3>Lists</h3>
      <p>Unordered</p>
      <pre>
* Item 1
* Item 2
  * Item 2a
  * Item 2b</pre>
     <p>Ordered</p>
     <pre>
1. Item 1
2. Item 2
3. Item 3
   * Item 3a
   * Item 3b</pre>
    </div>
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      <h3>Miscellaneous</h3>
      <p>Images</p>
      <pre>
![GitHub Logo](/images/logo.png)
Format: ![Alt Text](url)
</pre>
     <p>Links</p>
     <pre>
http://github.com - automatic!
[GitHub](http://github.com)</pre>
<p>Blockquotes</p>
     <pre>
As Kanye West said:

> We're living the future so
> the present is our past.
</pre>
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      <p>Syntax highlighting with <a href="http://github.github.com/github-flavored-markdown/" title="GitHub Flavored Markdown" target="_blank">GFM</a></p>
      <pre>
```javascript
function fancyAlert(arg) {
  if(arg) {
    $.facebox({div:'#foo'})
  }
}
```</pre>
    </div>
    <div class="col">
      <p>Or, indent your code 4 spaces</p>
      <pre>
Here is a Python code example
without syntax highlighting:

    def foo:
      if not bar:
        return true</pre>
    </div>
    <div class="col">
      <p>Inline code for comments</p>
      <pre>
I think you should use an
`&lt;addr&gt;` element here instead.</pre>
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Finally, my coworkers focus on flow cytometry data, and our group maintains several Bioconductor packages related to this type of data. To install the majority of them, we simply install the flowWorkspace package in R:

r source("http://bioconductor.org/biocLite.R") biocLite("flowWorkspace")

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