I am trying to run an example of JRI and being unsuccessful, here is a link to the example.
http://blog.comsysto.com/2013/07/10/java-r-integration-with-jri-for-on-demand-predictions/
import org.rosuda.JRI.Rengine;
import org.rosuda.JRI.REXP;
public class HelloRWorld {
Rengine rengine; // initialized in constructor or autowired
public void helloRWorld() {
rengine.eval(String.format("greeting <- '%s'", "Hello R World"));
REXP result = rengine.eval("greeting");
System.out.println("Greeting from R: "+result.asString());
}
}
This is the error the console gives me.
Exception in thread "main" java.lang.NullPointerException
at org.roulette.games.HelloRWorld.helloRWorld(HelloRWorld.java:10)
at org.roulette.games.HelloRWorld.main(HelloRWorld.java:17)
As far as I know I have the external JRI 2014-10-19 jar attached to the project correctly.
I have R 3.1.2 installed and I have the rJava 0.9-6 package installed.
Line 10 is "rengine.eval(String.format("greeting <- '%s'", "Hello R World"));".
And Line 17 is "hello.helloRWorld();".
Please Let me know if you have an idea as to why it's throwing these exceptions.... :)
Try this: is works:
package stackoverflow;
import org.rosuda.JRI.REXP;
import org.rosuda.JRI.Rengine;
/**
*
* @author yschellekens
*/
public class StackOverflow {
public static void main(String[] args) throws Exception {
String[] Rargs = {"--vanilla"};
Rengine rengine = new Rengine( Rargs, false, null);
rengine.eval("greeting <- '%Hello R World'");
REXP result = rengine.eval("greeting");
System.out.println("Greeting from R: "+result.asString());
}
}
Notice that you had several errors, including not including a main class, and not creating the proper constructor.
There are two different approach to connect Java and R.
If you want to use JRI, you have to start your java program using the JVM parameter -Djava.library.path pointing at the folder that contains JRI library.
For instance:
$JAVA_HOME/bin/java -Djava.library.path=/app/vendor/R/lib/R/library/rJava/jri/ -jar target/myapp.jar
If you have trouble finding JRI installation directory, try to look for the JRI SO library:
find / -name "libjri.*"
In addition, make sure you have created R_HOME and LD_LIBRARY_PATH in your environment:
- R_HOME: Pointing to your local R installation (Ej: /Library/Frameworks/R.framework/Resources)
- LD_LIBRARY_PATH: Pointing to R lib directory as well as JRI directory (EJ: $LD_LIBRARY_PATH:/app/vendor/R/lib/R/lib:/app/vendor/R/lib/R/bin)
Here is an example:
@Test
public void testMeanFunction() {
// just making sure we have the right version of everything
if (!Rengine.versionCheck()) {
System.err.println("** Version mismatch - Java files don't match library version.");
fail(String.format("Invalid versions. Rengine must have the same version of native library. Rengine version: %d. RNI library version: %d", Rengine.getVersion(), Rengine.rniGetVersion()));
}
// Enables debug traces
Rengine.DEBUG = 1;
System.out.println("Creating Rengine (with arguments)");
// 1) we pass the arguments from the command line
// 2) we won't use the main loop at first, we'll start it later
// (that's the "false" as second argument)
// 3) no callback class will be used
engine = REngine.engineForClass("org.rosuda.REngine.JRI.JRIEngine", new String[] { "--no-save" }, null, false);
System.out.println("Rengine created...");
engine.parseAndEval("rVector=c(1,2,3,4,5)");
REXP result = engine.parseAndEval("meanVal=mean(rVector)");
// generic vectors are RVector to accomodate names
assertThat(result.asDouble()).isEqualTo(3.0);
}
On the other hand, if you want to use Rserve, you need to start Rserve in a separate process, and then create a RConnection from your java process.
For example:
if(LOGGER.isInfoEnabled()) {
LOGGER.info("Starting RServe process...");
}
ProcessBuilder builder = new ProcessBuilder("/bin/sh", "-c", String.format("echo 'library(Rserve);Rserve(FALSE,args=\"--no-save --slave --RS-conf %s\")'|%s --no-save --slave", rserveConf, rexe));
builder.inheritIO();
Process rProcess = builder.start();
if(LOGGER.isInfoEnabled()) {
LOGGER.info("Waiting for Rserve to start...");
}
int execCodeResult = rProcess.waitFor();
if(execCodeResult != SUCCESS_CODE) {
LOGGER.error(String.format("Unexpected error code starting RServe: %d", execCodeResult));
} else {
LOGGER.error("RServe started successfully");
}
if(LOGGER.isInfoEnabled()) {
LOGGER.info("Opening connection to RServe daemon....");
}
REngine engine = new RConnection();
if(LOGGER.isInfoEnabled()) {
LOGGER.info(String.format("Obtaining R server version: %d", ((RConnection)engine).getServerVersion()));
}
//Perform some engine.parseAndEval("....");
rserveConf is the path to Rserv conf file and rexe is the full path to R executable.
For instance, in my MacOS computer I can start Rserve executing this line:
/bin/sh -c "echo 'library(Rserve);Rserve(FALSE,args=\"--slave --RS-conf /Users/me/Documents/test/rserve.conf\")'|/Library/Frameworks/R.framework/Versions/3.2/Resources/bin/exec/R --no-save --slave"
This command outputs something like this:
Starting Rserve:
/Library/Frameworks/R.framework/Resources/bin/R CMD /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rserve/libs//Rserve --slave
Rserv started in daemon mode.
Make sure to specify "--slave" parameter when you start Rserve.
If you want to see more examples, I have a demo project that use both approaches, JRI and RServe, in my github:
https://github.com/jfcorugedo/RJavaServer
You should export LD_LIBRARY_PATH by using below command
export LD_LIBRARY_PATH=/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/jre/lib/amd64/default
And from within R execute
install.packages("rJava")
That for sure will make your REngine works successfully from your java applicaition
