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POHow to connect to R with Java (using Eclipse)
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copied!<p>Very newbie (to Java) question:</p> <p>I opened an Rserve connection (<a href="http://www.rforge.net/Rserve/" rel="nofollow noreferrer">http://www.rforge.net/Rserve/</a>) on localhost, and I would like to use the REngine client (src/client/java-new in the Rserve package) to connect to it.</p> <p>What do I need to do to get the "RTest.java" (located in src/client/java-new/Rserve; pasted below) to compile?</p> <p>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). </p> <p>Anyone done this recently, care to offer a pointer? Thanks plenty.</p> <pre><code>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(); } } } </code></pre>

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