Author: jcouteau
Date: 2009-10-16 17:44:08 +0200 (Fri, 16 Oct 2009)
New Revision: 156
Modified:
trunk/src/main/java/org/nuiton/j2r/RProxy.java
trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java
Log:
Throw exception if jri not found
Modified: trunk/src/main/java/org/nuiton/j2r/RProxy.java
===================================================================
--- trunk/src/main/java/org/nuiton/j2r/RProxy.java 2009-10-16 13:30:37 UTC (rev 155)
+++ trunk/src/main/java/org/nuiton/j2r/RProxy.java 2009-10-16 15:44:08 UTC (rev 156)
@@ -50,9 +50,15 @@
/**
* Constructor. Launches the initialization.
+ *
+ * @throws RException if initialisation failed
*/
- public RProxy() {
- init();
+ public RProxy() throws RException {
+ Boolean init = init();
+ if (init == false) {
+ throw new RException(
+ "R initialisation failed, please check your installation");
+ }
}
/**
@@ -74,7 +80,7 @@
//if no success on net, tries on JNI
if (log.isErrorEnabled()) {
log.error(
- "Initialization of R with Network failed, trying JNI");
+ "Initialization of R with Network failed, trying JNI");
}
initSucceded = initOnJNI();
}
@@ -85,7 +91,7 @@
//if no success on jni, tries on net
if (log.isErrorEnabled()) {
log.error(
- "Initialization of R over JNI failed, trying with Network");
+ "Initialization of R over JNI failed, trying with Network");
}
initSucceded = initOnNet();
}
@@ -142,7 +148,7 @@
public Object eval(String expr) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return null;
}
return engine.eval(expr);
@@ -158,7 +164,7 @@
String rType = System.getProperty("R.type");
if (rType == null || "".equals(rType)) {
log.warn("No R type specified.\nusage:\n\tjava -DR.type=net ...\n" +
- "or\n\tjava -DR.type=jni ...\n\nConsidering network type");
+ "or\n\tjava -DR.type=jni ...\n\nConsidering network type");
rType = "net";
}
if (!init(rType)) {
@@ -179,7 +185,7 @@
public void terminate() throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
} else {
engine.terminate();
}
@@ -196,7 +202,7 @@
public void voidEval(String expr) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
engine.voidEval(expr);
@@ -216,7 +222,7 @@
public void loadRData(File directory) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
engine.setwd(directory);
@@ -237,7 +243,7 @@
public void saveRData(File directory) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
engine.setwd(directory);
@@ -258,7 +264,7 @@
public void setwd(File directory) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
engine.voidEval("setwd(\"" + directory.getAbsolutePath() + "\")");
@@ -279,7 +285,7 @@
public File getwd() throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return null;
}
return engine.getwd();
@@ -303,7 +309,7 @@
public void dput(String rObject, String outputFileName) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
String rInstruction = "dput(%s,file=\"%s\")";
@@ -329,7 +335,7 @@
public void dget(String rObject, String inputFileName) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
String rInstruction = "%s <- dget(\"%s\")";
@@ -353,14 +359,14 @@
public void dput(String rObject, File outputFile) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
File workingdir = getwd();
engine.setwd(outputFile.getParentFile());
String rInstruction = "dput(%s,file=\"%s\")";
engine.voidEval(String.format(rInstruction, rObject,
- outputFile.getName()));
+ outputFile.getName()));
setwd(workingdir);
}
@@ -381,14 +387,14 @@
public void dget(String rObject, File inputFile) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
File workingdir = getwd();
engine.setwd(inputFile.getParentFile());
String rInstruction = "%s <- dget(\"%s\")";
engine.voidEval(
- String.format(rInstruction, rObject, inputFile.getName()));
+ String.format(rInstruction, rObject, inputFile.getName()));
setwd(workingdir);
}
@@ -407,7 +413,7 @@
public void remove(String rObject) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
engine.remove(rObject);
@@ -430,7 +436,7 @@
public void mv(String source, String destination) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
engine.mv(source, destination);
@@ -454,7 +460,7 @@
public void cp(String inputObject, String outputObject) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
engine.cp(inputObject, outputObject);
@@ -476,7 +482,7 @@
public String[] ls() throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return null;
}
return engine.ls();
@@ -495,7 +501,7 @@
public void clearSession() throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
engine.clearSession();
@@ -515,7 +521,7 @@
public void commit() throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
engine.commit();
@@ -538,7 +544,7 @@
public void setAutoCommit(Boolean autocommit) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return;
}
engine.setAutoCommit(autocommit);
@@ -558,7 +564,7 @@
public Boolean isAutoCommit() {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
return null;
}
return engine.isAutoCommit();
@@ -582,7 +588,7 @@
public void saveRData(File directory, String fileName) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
}
engine.saveRData(directory, fileName);
}
@@ -606,8 +612,9 @@
public void loadRData(File directory, String fileName) throws RException {
if (engine == null) {
log.fatal("The R Proxy is not initialized. An error probably " +
- "occured during the initialization.");
+ "occured during the initialization.");
}
engine.loadRData(directory, fileName);
}
} //RProxy
+
Modified: trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java
===================================================================
--- trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java 2009-10-16 13:30:37 UTC (rev 155)
+++ trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java 2009-10-16 15:44:08 UTC (rev 156)
@@ -69,7 +69,21 @@
if (engine == null) {
try {
String[] args = {"--no-save"};
+
+ //Set the property so that rJava does not make a System.exit(1)
+ //System.setProperty("jri.ignore.ule", "yes");
+
+ //jriLoaded is false is rJava did not find jri library
+ if (!Rengine.jriLoaded) {
+ if (log.isErrorEnabled()) {
+ log.error(
+ "Cannot find jri library, make sure it is correctly installed");
+ }
+ return false;
+ }
+
engine = new Rengine(args, false, null);
+
if (!engine.waitForR()) {
if (log.isErrorEnabled()) {
log.error("Cannot load the R engine");
@@ -78,7 +92,7 @@
}
} catch (Exception eee) {
log.error("An error occured during R/JNI initialization.",
- eee);
+ eee);
return false;
}
}
@@ -107,7 +121,7 @@
//if the "class" attribute of the R expression is "try-error"
//throw a new exception with the error message from R.
String klass =
- result.getAttribute(RInstructions.ATTRIBUTE_CLASS).asString();
+ result.getAttribute(RInstructions.ATTRIBUTE_CLASS).asString();
if (klass.equals(RInstructions.CLASS_ERROR)) {
throw new RException(result.asString());
}
@@ -211,7 +225,7 @@
//get the class of the vector (to successfully detect data.frames)
String klass = "";
REXP klassAttribute = rexp.getAttribute(
- RInstructions.ATTRIBUTE_CLASS);
+ RInstructions.ATTRIBUTE_CLASS);
if (klassAttribute != null) {
klass = klassAttribute.asString();
}
@@ -224,7 +238,7 @@
//create the data list.
List<List<? extends Object>> data =
- new ArrayList<List<? extends Object>>();
+ new ArrayList<List<? extends Object>>();
//get rexp as a list (data.frame is a list of vectors)
org.rosuda.JRI.RList dataList = rexp.asList();
for (int i = 0; i < dataList.keys().length; i++) {
@@ -233,7 +247,7 @@
List<Object> templist = new ArrayList<Object>();
REXP tempREXP = dataList.at(i);
Object[] convertedREXP = (Object[]) convertResult(
- tempREXP);
+ tempREXP);
templist = Arrays.asList(convertedREXP);
//add this list to the data list.
data.add(templist);
@@ -243,9 +257,9 @@
//gotten from rexp. It has no variable name so throws a
//RException.
temp = new RDataFrame((REngine) this, rexp.getAttribute(
- RInstructions.ATTRIBUTE_NAMES).asStringArray(),
- rexp.getAttribute(RInstructions.ATTRIBUTE_ROWNAMES).asStringArray(),
- data, "");
+ RInstructions.ATTRIBUTE_NAMES).asStringArray(),
+ rexp.getAttribute(RInstructions.ATTRIBUTE_ROWNAMES).asStringArray(),
+ data, "");
result = temp;
} else if (list != null) {
RList temp = new RList((REngine) this);
@@ -255,7 +269,7 @@
//for each object of the list, convert it to java.
REXP tempREXP = dataList.at(i);
Object convertedREXP = (Object) convertResult(
- tempREXP);
+ tempREXP);
//add this object to the data list.
data.add(convertedREXP);
@@ -265,13 +279,13 @@
//RException.
try {
temp = new RList(
- rexp.getAttribute(RInstructions.ATTRIBUTE_NAMES).asStringArray(),
- data, (REngine) this, "");
+ rexp.getAttribute(RInstructions.ATTRIBUTE_NAMES).asStringArray(),
+ data, (REngine) this, "");
} catch (RException re) {
//don't propagate the error as it is normal. Log it for debug.
if (log.isDebugEnabled()) {
log.debug(
- "Converting REXP to RList. Creating list without variable name");
+ "Converting REXP to RList. Creating list without variable name");
}
}
result = temp;
@@ -283,7 +297,7 @@
default:
//if don't know the type, throw an exception.
log.error("Unknown return type [" + type + "] " + "on : " +
- rexp.toString());
+ rexp.toString());
break;
}
return result;
@@ -358,3 +372,4 @@
rInstructions = new LinkedList<String>();
}
} // RJniEngine
+
