How to connect to R with Java (using Eclipse)
https://stackoverflow.com/questions/1203662
italiano
english
français
española
中国
日本の
العربية
Deutsch
한국어
Português
RussianQuestion
Very newbie (to Java) question:
I opened an Rserve connection (http://www.rforge.net/Rserve/) on localhost, and I would like to use the REngine client (src/client/java-new in the Rserve package) to connect to it.
What do I need to do to get the "RTest.java" (located in src/client/java-new/Rserve; pasted below) to compile?
I gather that I need to compile the org.rosuda.* libraries. How can I do this using Eclipse 3.5? I tried copying the "src/client/java-new" folder into my Java project's "src" directory, right clicking in Eclipse -> Build path -> Use as source folder. But I don't think this is enough to create the "org.rosuda" package, because I don't see an "org/rosuda" directory structure created anywhere (and those ominous red lines in Eclipse don't disappear).
Anyone done this recently, care to offer a pointer? Thanks plenty.
import org.rosuda.REngine.*;
import org.rosuda.REngine.Rserve.*;
class TestException extends Exception {
public TestException(String msg) { super(msg); }
}
public class test {
public static void main(String[] args) {
try {
RConnection c = new RConnection();
System.out.println(">>"+c.eval("R.version$version.string").asString()+"<<");
{
System.out.println("* Test string and list retrieval");
RList l = c.eval("{d=data.frame(\"huhu\",c(11:20)); lapply(d,as.character)}").asList();
int cols = l.size();
int rows = l.at(0).length();
String[][] s = new String[cols][];
for (int i=0; i<cols; i++) s[i]=l.at(i).asStrings();
System.out.println("PASSED");
}
{
System.out.println("* Test NA/NaN support in double vectors...");
double R_NA = Double.longBitsToDouble(0x7ff00000000007a2L);
// int R_NA_int = -2147483648; // just for completeness
double x[] = { 1.0, 0.5, R_NA, Double.NaN, 3.5 };
c.assign("x",x);
String nas = c.eval("paste(capture.output(print(x)),collapse='\\n')").asString();
System.out.println(nas);
if (!nas.equals("[1] 1.0 0.5 NA NaN 3.5"))
throw new TestException("NA/NaN assign+retrieve test failed");
System.out.println("PASSED");
}
{
System.out.println("* Test assigning of lists and vectors ...");
RList l = new RList();
l.put("a",new REXPInteger(new int[] { 0,1,2,3}));
l.put("b",new REXPDouble(new double[] { 0.5,1.2,2.3,3.0}));
System.out.println(" assign x=pairlist");
c.assign("x", new REXPList(l));
System.out.println(" assign y=vector");
c.assign("y", new REXPGenericVector(l));
System.out.println(" assign z=data.frame");
c.assign("z", REXP.createDataFrame(l));
System.out.println(" pull all three back to Java");
REXP x = c.parseAndEval("x");
System.out.println(" x = "+x);
x = c.eval("y");
System.out.println(" y = "+x);
x = c.eval("z");
System.out.println(" z = "+x);
System.out.println("PASSED");
}
{
System.out.println("* Test support for logicals ... ");
System.out.println(" assign b={true,false,true}");
c.assign("b", new REXPLogical(new boolean[] { true, false, true }));
REXP x = c.parseAndEval("b");
System.out.println(" " + ((x != null) ? x.toDebugString() : "NULL"));
if (!x.isLogical() || x.length() != 3)
throw new TestException("boolean array assign+retrieve test failed");
boolean q[] = ((REXPLogical)x).isTRUE();
if (q[0] != true || q[1] != false || q[2] != true)
throw new TestException("boolean array assign+retrieve test failed (value mismatch)");
System.out.println(" get c(TRUE,FLASE,NA)");
x = c.parseAndEval("c(TRUE,FALSE,NA)");
System.out.println(" " + ((x != null) ? x.toDebugString() : "NULL"));
if (!x.isLogical() || x.length() != 3)
throw new TestException("boolean array NA test failed");
boolean q1[] = ((REXPLogical)x).isTRUE();
boolean q2[] = ((REXPLogical)x).isFALSE();
boolean q3[] = ((REXPLogical)x).isNA();
if (q1[0] != true || q1[1] != false || q1[2] != false ||
q2[0] != false || q2[1] != true || q2[2] != false ||
q3[0] != false || q3[1] != false || q3[2] != true)
throw new TestException("boolean array NA test failed (value mismatch)");
}
{ // regression: object bit was not set for Java-side generated objects before 0.5-3
System.out.println("* Testing functionality of assembled S3 objects ...");
// we have already assigned the data.frame in previous test, so we jsut re-use it
REXP x = c.parseAndEval("z[2,2]");
System.out.println(" z[2,2] = " + x);
if (x == null || x.length() != 1 || x.asDouble() != 1.2)
throw new TestException("S3 object bit regression test failed");
System.out.println("PASSED");
}
{ // this test does a pull and push of a data frame. It will fail when the S3 test above failed.
System.out.println("* Testing pass-though capability for data.frames ...");
REXP df = c.parseAndEval("{data(iris); iris}");
c.assign("df", df);
REXP x = c.eval("identical(df, iris)");
System.out.println(" identical(df, iris) = "+x);
if (x == null || !x.isLogical() || x.length() != 1 || !((REXPLogical)x).isTrue()[0])
throw new TestException("Pass-through test for a data.frame failed");
System.out.println("PASSED");
}
{ // factors
System.out.println("* Test support of factors");
REXP f = c.parseAndEval("factor(paste('F',as.integer(runif(20)*5),sep=''))");
System.out.println(" f="+f);
System.out.println(" isFactor: "+f.isFactor()+", asFactor: "+f.asFactor());
if (!f.isFactor() || f.asFactor() == null) throw new TestException("factor test failed");
System.out.println(" singe-level factor used to degenerate:");
f = c.parseAndEval("factor('foo')");
System.out.println(" isFactor: "+f.isFactor()+", asFactor: "+f.asFactor());
if (!f.isFactor() || f.asFactor() == null) throw new TestException("single factor test failed (not a factor)");
if (!f.asFactor().at(0).equals("foo")) throw new TestException("single factor test failed (wrong value)");
System.out.println(" test factors with null elements contents:");
c.assign("f", new REXPFactor(new RFactor(new String[] { "foo", "bar", "foo", "foo", null, "bar" })));
f = c.parseAndEval("f");
if (!f.isFactor() || f.asFactor() == null) throw new TestException("factor assign-eval test failed (not a factor)");
System.out.println(" f = "+f.asFactor());
f = c.parseAndEval("as.factor(c(1,'a','b',1,'b'))");
System.out.println(" f = "+f);
if (!f.isFactor() || f.asFactor() == null) throw new TestException("factor test failed (not a factor)");
System.out.println("PASSED");
}
{
System.out.println("* Lowess test");
double x[] = c.eval("rnorm(100)").asDoubles();
double y[] = c.eval("rnorm(100)").asDoubles();
c.assign("x", x);
c.assign("y", y);
RList l = c.parseAndEval("lowess(x,y)").asList();
System.out.println(" "+l);
x = l.at("x").asDoubles();
y = l.at("y").asDoubles();
System.out.println("PASSED");
}
{
// multi-line expressions
System.out.println("* Test multi-line expressions");
if (c.eval("{ a=1:10\nb=11:20\nmean(b-a) }\n").asInteger()!=10)
throw new TestException("multi-line test failed.");
System.out.println("PASSED");
}
{
System.out.println("* Matrix tests\n matrix: create a matrix");
int m=100, n=100;
double[] mat=new double[m*n];
int i=0;
while (i<m*n) mat[i++]=i/100;
System.out.println(" matrix: assign a matrix");
c.assign("m", mat);
c.voidEval("m<-matrix(m,"+m+","+n+")");
System.out.println("matrix: cross-product");
double[][] mr=c.parseAndEval("crossprod(m,m)").asDoubleMatrix();
System.out.println("PASSED");
}
{
System.out.println("* Test serialization and raw vectors");
byte[] b = c.eval("serialize(ls, NULL, ascii=FALSE)").asBytes();
System.out.println(" serialized ls is "+b.length+" bytes long");
c.assign("r", new REXPRaw(b));
String[] s = c.eval("unserialize(r)()").asStrings();
System.out.println(" we have "+s.length+" items in the workspace");
System.out.println("PASSED");
}
{ // string encoding test (will work with Rserve 0.5-3 and higher only)
System.out.println("* Test string encoding support ...");
String t = "ひらがな"; // hiragana (literally, in hiragana ;))
c.setStringEncoding("utf8");
// -- Just in case the console is not UTF-8 don't display it
//System.out.println(" unicode text: "+t);
c.assign("s", t);
REXP x = c.parseAndEval("nchar(s)");
System.out.println(" nchar = " + x);
if (x == null || !x.isInteger() || x.asInteger() != 4)
throw new TestException("UTF-8 encoding string length test failed");
// we cannot really test any other encoding ..
System.out.println("PASSED");
}
} catch (RserveException rse) {
System.out.println(rse);
} catch (REXPMismatchException mme) {
System.out.println(mme);
mme.printStackTrace();
} catch(TestException te) {
System.err.println("** Test failed: "+te.getMessage());
te.printStackTrace();
} catch (Exception e) {
e.printStackTrace();
}
}
}
Solution
I cannot help you with the Java aspect, besides noting that on my Linux machine, simply calling make does the trick:
/tmp/java-new$ make
javac -d . -source 1.4 -target 1.4 MutableREXP.java REngineException.java REngine.java REXPDouble.java REXPEnvironment.java REXPExpressionVector.java REXPFactor.java REXPGenericVector.java REXPInteger.java REXP.java REXPLanguage.java REXPList.java REXPLogical.java REXPMismatchException.java REXPNull.java REXPRaw.java REXPReference.javaREXPS4.java REXPString.java REXPSymbol.java REXPUnknown.java REXPVector.java RFactor.java RList.java
jar fc REngine.jar org
rm -rf org
javac -d . -cp REngine.jar Rserve/RConnection.java Rserve/RFileInputStream.java Rserve/RFileOutputStream.java Rserve/RserveException.java Rserve/RSession.java Rserve/protocol/jcrypt.java Rserve/protocol/REXPFactory.java Rserve/protocol/RPacket.java Rserve/protocol/RTalk.java
Note: Rserve/protocol/REXPFactory.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
jar fc Rserve.jar org
rm -rf org
Likewise with the example directory you mentioned -- it builds fine on my Linux machine just saying 'make'. I do not use Eclipse and can't help with that aspect.
The C++ examples also run fine as well (though I needed to adjust the Makefile to build them).
You may need to ask to the Rosuda list for Rserv.
OTHER TIPS
Yes, indeed. Compile the JAR just as Dirk indicated, then in Eclipse right click -> Add to Build Path, and the org.rosuda.* package gets created and can be imported as in the examples.
FWIW the JAR files are also available directly from the Rserve website: http://www.rforge.net/Rserve/files/
And yes, "make" is all you need to run to create the JAR files from the sources (works on any platform including Windows).
Licensed under: CC-BY-SA with attribution
Not affiliated with StackOverflow
