"Can not install R - extension with R 2.13"

himanshubdave

echo $R_HOME
/usr/local/lib/R

echo $JAVA_HOME
/usr/lib/java

echo $PATH
<snip>
/Reader9/bin/:/usr/lib/jdk1.6.0_25/bin/:/usr/local/lib/R/bin

> .libPaths()
[1] "/usr/local/lib/R/library"

When rapidminer invoked, it says:
...  ...  ...
SEVERE: Failed to load R library!

and R-extension help window comes up, on pressing Next, it says:
Found library in /usr/local/lib/R/library/rJava/jri/REngine.jar

The R-extension help window says:
Exit now, rapidminer will restart. (It does not, manual restart)

and the whole thing repeats.

Clueless, please help

MariusHelf

Hm, are you using the latest version of RapidMiner (5.2.6) and the R extension (5.1.4)?

Best, Marius

cbwq

I get something quite similar.
Ubuntu 10.04lts with R version 2.15.0 (2012-03-30) installed from cran mirror/lucid
Rapid miner 5.2.006 and R extension 5.1.004.

When started from console, the below exception is thrown in RapidMiner's startup spam.

RapidMiner, platform ANY
05/06/2012 5:04:33 PM com.rapidminer.tools.ParameterService init
INFO: Reading configuration resource com/rapidminer/resources/rapidminerrc.
05/06/2012 5:04:33 PM com.rapidminer.tools.I18N <clinit>
INFO: Set locale to en.
05/06/2012 5:04:34 PM com.rapid_i.Launcher ensureRapidMinerHomeSet
INFO: rapidminer.home is '.'.
05/06/2012 5:04:35 PM com.rapidminer.PluginInitR initPlugin
INFO: Trying to load R Library...
05/06/2012 5:04:35 PM org.rosuda.JRI.Rengine <clinit>
INFO: Creating Connection to R...
05/06/2012 5:04:35 PM org.rosuda.JRI.Rengine loadLibrary
INFO: Trying to loaded R library from /usr/lib/R/site-library/rJava/jri/libjri.so
05/06/2012 5:04:35 PM org.rosuda.JRI.Rengine loadLibrary
INFO: Engine ID: class org.rosuda.JRI.Rengine ClassLoader:PluginClassLoader ([file:/home/user/.RapidMiner5/managed/rmx_r-5.1.4.jar])
05/06/2012 5:04:36 PM org.rosuda.JRI.Rengine loadLibrary
INFO: Successfully loaded R library from /usr/lib/R/site-library/rJava/jri/libjri.so(true)
05/06/2012 5:04:41 PM com.rapidminer.parameter.ParameterTypePassword decryptPassword
WARNING: Password in XML file looks like unencrypted plain text.
[Fatal Error] :1:1: Content is not allowed in prolog.
05/06/2012 5:04:46 PM com.rapidminer.operator.r.ROperatorFactory readROperatorFragments
WARNING: Could not read R fragments from 'file:/opt/rapidminer/', error: Content is not allowed in prolog.
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at com.rapidminer.io.process.XMLTools.parse(XMLTools.java:176)
	at com.rapidminer.operator.r.ROperatorFactory.readROperatorFragments(ROperatorFactory.java:166)
	at com.rapidminer.operator.r.ROperatorFactory.<init>(ROperatorFactory.java:129)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
	at java.lang.Class.newInstance0(Class.java:372)
	at java.lang.Class.newInstance(Class.java:325)
	at com.rapidminer.tools.OperatorService.parseOperators(OperatorService.java:362)
	at com.rapidminer.tools.OperatorService.parseOperators(OperatorService.java:269)
	at com.rapidminer.tools.OperatorService.registerOperators(OperatorService.java:231)
	at com.rapidminer.tools.plugin.Plugin.registerOperators(Plugin.java:483)
	at com.rapidminer.tools.plugin.Plugin.registerAllPluginOperators(Plugin.java:782)
	at com.rapidminer.tools.OperatorService.init(OperatorService.java:182)
	at com.rapidminer.RapidMiner.init(RapidMiner.java:508)
	at com.rapidminer.gui.RapidMinerGUI.run(RapidMinerGUI.java:218)
	at com.rapidminer.gui.RapidMinerGUI.launch(RapidMinerGUI.java:523)
	at com.rapidminer.gui.RapidMinerGUI.main(RapidMinerGUI.java:505)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:616)
	at com.rapid_i.Launcher.main(Launcher.java:334)
[Fatal Error] :1:1: Content is not allowed in prolog.
05/06/2012 5:04:46 PM com.rapidminer.operator.r.ROperatorFactory <init>
WARNING: Could not read documentation of user defined R operators from .
java.io.IOException: Malformed XML operator help bundle: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.rapidminer.tools.documentation.XMLOperatorDocBundle.<init>(XMLOperatorDocBundle.java:129)
	at com.rapidminer.operator.r.ROperatorFactory.<init>(ROperatorFactory.java:150)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
	at java.lang.Class.newInstance0(Class.java:372)
	at java.lang.Class.newInstance(Class.java:325)
	at com.rapidminer.tools.OperatorService.parseOperators(OperatorService.java:362)
	at com.rapidminer.tools.OperatorService.parseOperators(OperatorService.java:269)
	at com.rapidminer.tools.OperatorService.registerOperators(OperatorService.java:231)
	at com.rapidminer.tools.plugin.Plugin.registerOperators(Plugin.java:483)
	at com.rapidminer.tools.plugin.Plugin.registerAllPluginOperators(Plugin.java:782)
	at com.rapidminer.tools.OperatorService.init(OperatorService.java:182)
	at com.rapidminer.RapidMiner.init(RapidMiner.java:508)
	at com.rapidminer.gui.RapidMinerGUI.run(RapidMinerGUI.java:218)
	at com.rapidminer.gui.RapidMinerGUI.launch(RapidMinerGUI.java:523)
	at com.rapidminer.gui.RapidMinerGUI.main(RapidMinerGUI.java:505)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:616)
	at com.rapid_i.Launcher.main(Launcher.java:334)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at com.rapidminer.tools.documentation.XMLOperatorDocBundle.<init>(XMLOperatorDocBundle.java:127)
	... 22 more
...
Stuff about database drivers
...
initGui(MainFrame mainFrame)
cannot find system Renviron
ARGUMENT 'LANGUAGE=en' __ignored__

RapidMiner will now relaunch

Then the loop commences.

Any idea what I'm doing wrong?