Q: Calling R in java-Rcaller I am trying to implement clustering using R in java by employing R caller. I am trying to run sample code for clustering validation and I get that common error faced by most of the users: Premature end of file
package test;
import rcaller.RCaller;
import java.io.File;
import java.lang.*;
import java.util.*;
import java.awt.image.DataBuffer;

public class test3 {
    public static void main(String[] args) {
        new test3();
    }

    public test3()
    {

        try{

            RCaller caller = new RCaller();
            caller.cleanRCode();

            caller.setRscriptExecutable("C:/Program Files/R/R-2.15.1/bin/x64/Rscript");
            caller.cleanRCode();

            caller.addRCode("library(clvalid)");
            caller.addRCode("data(mouse)");
            caller.addRCode("express <- mouse [,c(M1,M2,M3,NC1,NC2,NC3)]");
            caller.addRCode("rownames (express) <- mouse$ID ");
            caller.addRCode("intern <- clValid(express, 2:6 , clMethods = c( hierarchical,kmeans,diana,clara,model) ,validation = internal)");
            caller.addRCode("b <- summary(intern) ");
            caller.runAndReturnResult("b");
        }

        catch (Exception e){
            e.printStackTrace();
        }
    }
}


A: You have some spelling mistakes in you code. like clValid not clvalid  , and you miss many quotes like "hierarchical",....
I think it is better to put your code in a script, and call it from java like this : 
Runtime.getRuntime().exec("Rscript myScript.R"); 

where myScript.R is : 
library(clValid)
data(mouse)
express <- mouse [,c('M1','M2','M3','NC1','NC2','NC3')]
rownames (express) <- mouse$ID 
intern <- clValid(express, 2:6 , clMethods = c( 'hierarchical','kmeans',
                                               'diana','clara','model') ,
                                                validation = 'internal')
b <- summary(intern) 

