Remove unused dependencies

Current dependencies:

RJSONIO (>= 0.96-0),  
plyr (>= 1.7.1),      
data.table (>= 1.8.2),
MASS (>= 7.3-22),     
classInt (>= 0.1-19), 
ggplot2 (>= 0.9.3),   
labeling (>= 0.1),    
XML (>= 3.0)          

Some of the dependencies could be removed. This might require removing functions that are not working any more.