Getting RStudio to work with RWeka and the previous java 1.8 problem

So, from the previous post, installing Java 1.6 and recompiling rJava is enough to get everything working from a terminal window. But, if you start up RStudio and try to use RWeka (or other libraries using JNI, probably) you'll see an error message similar to:

Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/Cellar/r/3.2.0_1/R.framework/Versions/3.2/Resources/library/rJava/libs/rJava.so':
  dlopen(/usr/local/Cellar/r/3.2.0_1/R.framework/Versions/3.2/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
  Referenced from: /usr/local/Cellar/r/3.2.0_1/R.framework/Versions/3.2/Resources/library/rJava/libs/rJava.so
  Reason: image not found
Error: package or namespace load failed for ‘RWeka’

A workaround is to start RStudio from a terminal window by running the following line:

LD_LIBRARY_PATH=$(/usr/libexec/java_home)/jre/lib/server: open -a RStudio

Getting various R packages to work with Java 1.8 and rJava on OSX

If you attempt to install various R packages (e.g. RWeka) on OSX using a Java 1.8 runtime, you're likely to run into the following error message (even though you have a perfectly good installation of Java):

"No Java runtime present, requesting install.
ERROR: loading failed"

There are a ton of threads out there about this problem, but it seems to boil down to this unclosed (and untouched since 2014-01) JDK issue -> https://bugs.openjdk.java.net/browse/JDK-7131356

The "solution" can be found on the last comment on this rJava github issue: https://github.com/s-u/rJava/issues/37

1. install JDK 1.6 from Apple (http://support.apple.com/kb/DL1572)
2. open a new terminal window and make sure you're still using 1.8 - "java -version"
3. run "sudo R CMD javareconf -n" from a terminal window
4. start up R and install rJava again from source - install.packages("rJava", type="source")

Continuous integration: Rmd to md to html

I'm taking one of the Coursera courses right now on Reproducible Research and the first assignment requires you to build an Rmd file and convert it to html (using knitr). They do a really good job showing how to use RStudio to accomplish this task, but what if you don't want to bother with RStudio?

Here's (https://gist.github.com/slowteetoe/7b8426f567ac3df1d8f9) a simple bash script that watches an Rmd file. When you save that file, it runs knitr to convert it to markdown, and then converts the markdown to html and opens it in a browser... sorta a continuous integration for R markdown.

Couple caveats: you'll need to install the Ruby gem 'kicker', the r packages 'knitr' and 'markdown', and put this script somewhere in your path. It will also have to be made executable, 'chmod 755 knitr'. Also, it opens a different browser tab each time - but I couldn't figure out how to change this behavior and it was worth it (to me at least).

R annoyances

R seems to be, hmm, quirky, from what I've seen of it so far... For instance, ddply has different behavior using the American vs. British spellings of "summarize". Seriously?!

> g <- ddply(m, c("QGroup","Income.Group"), summarize, All = length(CountryCode))
Error: argument "by" is missing, with no default

> g <- ddply(m, c("QGroup","Income.Group"), summarise, All = length(CountryCode))

Yes, that's right - "summarise" works fine but "summarize" apparently takes different arguments.

Trouble installing jpeg R package on OSX?

I'm taking the Coursera "Getting and Cleaning Data" class in R and one of the quizzes requires you to use the jpeg package. The R package install was failing for some reason though:

install.packages("jpeg")

In file included from read.c:1:
./rjcommon.h:11:10: fatal error: 'jpeglib.h' file not found
#include 
         ^

I use homebrew, so I tried the usual...

brew install jpeg
Warning: jpeg-8d already installed

brew unlink jpeg && brew link jpeg

But that didn't fix the issue. The solution was to install the XCode command line tools with:

xcode-select --install

(As a side note, this is my development machine so I already had XCode command line tools but for whatever reason I had to install them again, maybe an XCode upgrade?)