"Can not install R - extension with R 2.13"

himanshubdave
himanshubdave New Altair Community Member
edited November 5 in Community Q&A
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
Tagged:

Answers

  • MariusHelf
    MariusHelf New Altair Community Member
    Hm, are you using the latest version of RapidMiner (5.2.6) and the R extension (5.1.4)?

    Best, Marius
  • cbwq
    cbwq New Altair Community Member
    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?

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