External Program execution problems

[vital101]

Hey everyone,

I'm working on a project right now where I need to be able to access an external program from inside my Java app. My problem is that as soon as i launch the program, any other commands I issue are treated and strictly command line actions and are not executed inside the program. Here's what i've got.

Code:

import java.io.*;

public class ExecDemoWait {

  public static void main(String argv[]) throws IOException {

    Runtime r = Runtime.getRuntime();
    Process p;     // Process tracks one external native process
    BufferedReader is;  // reader for output of process
    String line;

   /******************************
    * PROBLEM IS IN THE NEXT TWO LINES
    ******************************/
    p = r.exec("R --no-save");
    p = r.exec("seq(1,3,1)");

    System.out.println("In Main after exec");
    is = new BufferedReader(new InputStreamReader(p.getInputStream()));

    while ((line = is.readLine()) != null)
      System.out.println(line);
    
    System.out.println("In Main after EOF");
    System.out.flush();
    try {
      p.waitFor();  // wait for process to complete
    } catch (InterruptedException e) {
      System.err.println(e);  // "Can'tHappen"
      return;
    }
    System.err.println("Process done, exit status was " + p.exitValue());
    return;
  }
}

As you can see, I first launch R, then I try and execute a statement that produces a sequence of numbers. However, when I run the program I get...

Quote:

Exception in thread "main" java.io.IOException: Cannot run program "seq(1,3,1)": java.io.IOException: error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java :459)
at java.lang.Runtime.exec(Runtime.java:593)
at java.lang.Runtime.exec(Runtime.java:431)
at java.lang.Runtime.exec(Runtime.java:328)
at ExecDemoWait.main(ExecDemoWait.java:23)
Caused by: java.io.IOException: java.io.IOException: error=2, No such file or directory
at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
at java.lang.ProcessImpl.start(ProcessImpl.java:65)
at java.lang.ProcessBuilder.start(ProcessBuilder.java :452)
... 4 more

From the first line, we can see that it's trying to run the "sequence.." argument as a stand-alone command line argument. How can I get the "sequence.." command to execute inside of R?

Thanks for the help.
/vital101

[JavaBean]

I guess you will need to get input stream of the process and write your commands through it. Search internet for examples to use input streams of the processes.

[vital101]

Do you think it'd be possible to do something like:

Code:

p = r.exec("R --no-save < test.r");
//where test.r contains seq(1,10,1)

When I do this on the command line directly, it works fine. However, when I do this from within Java, it ignores (and tells me it's ignoring) everything from the "<" forward. Here's the error:

Quote:

In Main after exec
ARGUMENT '<' __ignored__

ARGUMENT 'test.r' __ignored__


R version 2.5.1 (2007-06-27)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
....

[JavaBean]

Yes, i am sure it is possible but it is not working as in the first way we think.

Check the following way for several examples. As far as i see (after a quick look), the page also has examples for processes with parameters...

Execute an external program - Real's Java How-to