Hello Guys!!
I am trying to run the ArrayQualityMetrics Rscript from my java code. But it is not running through the java code
Any suggestions please are appreciated ........

my java code is:-

    public class TestClass {
         public static void main(String[] args) {
        // TODO Auto-generated method stub

        try{    
            Process p = Runtime.getRuntime().exec("C:/R/R-3.2.0/bin/Rscript array.R");

                        int processComplete = p.waitFor();

                           if (processComplete == 0) { 
                                System.out.println("successfull");
                           } else {
                              System.out.println("Could not complete");
                           }
                        }
                        catch (Exception e)
                        {
                                       e.printStackTrace();
                                    }
         }
    }

I am not getting why am I getting the else output :- "Could not complete" while runnig the java code

I want to know why the messages are comming after the library(arrayQualityMetrics)

 Creating a generic function for ‘boxplot’ from package ‘graphics’ in package ‘affyPLM’
 Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’

Help me out. I am not getting where am I getting wrong....Do reply..
Thank you...

No idea about the return value from java. If the R code runs successfully then this is really a question about getting java to work, not arrayQualityMetrics.

As for the messages, they mean pretty much what they say. There are hist and boxplot functions in the graphics package, and when you load affyPLM, it is creating generic functions, based on the existing functions from the graphics package:

> hist
function (x, ...)
UseMethod("hist")
<bytecode: 0x2e0b718>
<environment: namespace:graphics>
> boxplot
function (x, ...)
UseMethod("boxplot")
<bytecode: 0x1e88988>
<environment: namespace:graphics>

> library(affyPLM)

> hist
standardGeneric for "hist" defined from package "graphics"

function (x, ...)
standardGeneric("hist")
<environment: 0x41984d0>
Methods may be defined for arguments: x
Use  showMethods("hist")  for currently available ones.
> boxplot
standardGeneric for "boxplot" defined from package "graphics"

function (x, ...)
standardGeneric("boxplot")
<environment: 0x22ca1e8>
Methods may be defined for arguments: x
Use  showMethods("boxplot")  for currently available ones.

In other words, hist() and boxplot() are S3 methods in the graphics package, and affyPLM creates S4 methods based on the existing S3 packages. S3 is an earlier object oriented programming paradigm used in R (some might argue that it isn't really OO at all), and S4 is a more modern version of OO programming.