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R extension
danjeharry
Member Posts: 20 
Contributor II
Hey all,
I tried to get the R extension working for rapid miner and ran into some very odd issues. Basically my rapid miner starts up but the GUI never shows. I'm usiing the .bat shell program to start rapidminer and this is the output I see:
Note sure what's going on here. I'm pretty sure I have all my environmental variables and directories set correct as it seems to find the rapid miner libraries etc.
RAPIDMINER_HOME is not set. Trying the directory 'C:\Program Files\Rapid-I\Rapid
Miner5\scripts\..'...
Using local jre: C:\Program Files\Rapid-I\RapidMiner5\scripts\..\jre\bin\java.ex
e...
Starting RapidMiner from 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..' using
classes from 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..\lib\rapidminer.ja
r'...
Oct 28, 2011 9:30:45 AM com.rapid_i.Launcher ensureRapidMinerHomeSet
INFO: rapidminer.home is 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..'.
Oct 28, 2011 9:30:45 AM com.rapid_i.Launcher main
INFO: Launching RapidMiner, platform WIN64
Oct 28, 2011 9:30:46 AM com.rapid_i.Launcher ensureRapidMinerHomeSet
INFO: rapidminer.home is 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..'.
Oct 28, 2011 9:30:46 AM com.rapidminer.tools.ParameterService init
INFO: Reading configuration resource com/rapidminer/resources/rapidminerrc.
Oct 28, 2011 9:30:46 AM com.rapidminer.PluginInitR initPlugin
INFO: Trying to load R Library...
Oct 28, 2011 9:30:46 AM org.rosuda.JRI.Rengine <clinit>
INFO: Creating Connection to R...
Oct 28, 2011 9:30:46 AM org.rosuda.JRI.Rengine loadLibrary
INFO: Trying to loaded R library from C:\Program Files\R\R-2.13.1\library\rJava\
jri\x64\jri.dll
Oct 28, 2011 9:30:46 AM org.rosuda.JRI.Rengine loadLibrary
INFO: Engine ID: class org.rosuda.JRI.Rengine ClassLoader:PluginClassLoader ([fi
le:/C:/Documents%20and%20Settings/swang8/.RapidMiner5/managed/rmx_r-5.1.4.jar])
Oct 28, 2011 9:30:46 AM org.rosuda.JRI.Rengine loadLibrary
INFO: Successfully loaded R library from C:\Program Files\R\R-2.13.1\library\rJa
va\jri\x64\jri.dll(true)
Oct 28, 2011 9:30:48 AM com.rapidminer.parameter.ParameterTypePassword decryptPa
ssword
WARNING: Password in XML file looks like unencrypted plain text.
[Fatal Error] :1:1: Content is not allowed in prolog.
Oct 28, 2011 9:30:50 AM com.rapidminer.operator.r.ROperatorFactory readROperator
Fragments
WARNING: Could not read R fragments from 'file:/C:/Program%20Files/Rapid-I/Rapid
Miner5/scripts/', error: Content is not allowed in prolog.
org.xml.sax.SAXParseException: Content is not allowed in prolog.
at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown So
urce)
at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unk
nown Source)
at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
at com.rapidminer.io.process.XMLTools.parse(XMLTools.java:175)
at com.rapidminer.operator.r.ROperatorFactory.readROperatorFragments(ROp
eratorFactory.java:166)
at com.rapidminer.operator.r.ROperatorFactory.<init>(ROperatorFactory.ja
va:129)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Sou
rce)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at java.lang.Class.newInstance0(Unknown Source)
at java.lang.Class.newInstance(Unknown Source)
at com.rapidminer.tools.OperatorService.parseOperators(OperatorService.j
ava:294)
at com.rapidminer.tools.OperatorService.parseOperators(OperatorService.j
ava:232)
at com.rapidminer.tools.OperatorService.registerOperators(OperatorServic
e.java:206)
at com.rapidminer.tools.plugin.Plugin.registerOperators(Plugin.java:471)
at com.rapidminer.tools.plugin.Plugin.registerAllPluginOperators(Plugin.
java:725)
at com.rapidminer.tools.OperatorService.init(OperatorService.java:167)
at com.rapidminer.RapidMiner.init(RapidMiner.java:465)
at com.rapidminer.gui.RapidMinerGUI.run(RapidMinerGUI.java:221)
at com.rapidminer.gui.RapidMinerGUI.launch(RapidMinerGUI.java:505)
at com.rapidminer.gui.RapidMinerGUI.main(RapidMinerGUI.java:488)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.rapid_i.Launcher.main(Launcher.java:334)
[Fatal Error] :1:1: Content is not allowed in prolog.
Oct 28, 2011 9:30:50 AM 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.SAXParseExc
eption: Content is not allowed in prolog.
at com.rapidminer.tools.documentation.XMLOperatorDocBundle.<init>(XMLOpe
ratorDocBundle.java:119)
at com.rapidminer.operator.r.ROperatorFactory.<init>(ROperatorFactory.ja
va:150)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Sou
rce)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at java.lang.Class.newInstance0(Unknown Source)
at java.lang.Class.newInstance(Unknown Source)
at com.rapidminer.tools.OperatorService.parseOperators(OperatorService.j
ava:294)
at com.rapidminer.tools.OperatorService.parseOperators(OperatorService.j
ava:232)
at com.rapidminer.tools.OperatorService.registerOperators(OperatorServic
e.java:206)
at com.rapidminer.tools.plugin.Plugin.registerOperators(Plugin.java:471)
at com.rapidminer.tools.plugin.Plugin.registerAllPluginOperators(Plugin.
java:725)
at com.rapidminer.tools.OperatorService.init(OperatorService.java:167)
at com.rapidminer.RapidMiner.init(RapidMiner.java:465)
at com.rapidminer.gui.RapidMinerGUI.run(RapidMinerGUI.java:221)
at com.rapidminer.gui.RapidMinerGUI.launch(RapidMinerGUI.java:505)
at com.rapidminer.gui.RapidMinerGUI.main(RapidMinerGUI.java:488)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.rapid_i.Launcher.main(Launcher.java:334)
Caused by: org.xml.sax.SAXParseException: Content is not allowed in prolog.
at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown So
urce)
at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unk
nown Source)
at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
at com.rapidminer.tools.documentation.XMLOperatorDocBundle.<init>(XMLOpe
ratorDocBundle.java:117)
... 22 more
Oct 28, 2011 9:30:50 AM com.rapidminer.tools.plugin.Plugin registerOperators
INFO: No operator descriptor specified for plugin Community. Trying plugin initi
aliztation class com.rapidminer.community.CommunityPluginInit.
Oct 28, 2011 9:30:50 AM com.rapidminer.tools.plugin.Plugin registerOperators
WARNING: No operator descriptor defined for: Community
Oct 28, 2011 9:30:51 AM com.rapidminer.tools.jdbc.JDBCProperties <init>
WARNING: Missing database driver class name for 'ODBC Bridge (e.g. Access)'
Oct 28, 2011 9:30:51 AM com.rapidminer.tools.jdbc.JDBCProperties registerDrivers
INFO: JDBC driver ca.ingres.jdbc.IngresDriver not found. Probably the driver is
not installed.
Oct 28, 2011 9:30:51 AM com.rapidminer.tools.jdbc.JDBCProperties registerDrivers
INFO: JDBC driver oracle.jdbc.driver.OracleDriver not found. Probably the driver
is not installed.
initGui(MainFrame mainFrame)
Starting RapidMiner from 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..' using
classes from 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..\lib\rapidminer.ja
r'...
Oct 28, 2011 9:30:53 AM com.rapid_i.Launcher ensureRapidMinerHomeSet
INFO: rapidminer.home is 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..'.
Oct 28, 2011 9:30:53 AM com.rapid_i.Launcher main
INFO: Launching RapidMiner, platform WIN64
Oct 28, 2011 9:30:55 AM com.rapid_i.Launcher ensureRapidMinerHomeSet
INFO: rapidminer.home is 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..'.
Oct 28, 2011 9:30:55 AM com.rapidminer.tools.ParameterService init
INFO: Reading configuration resource com/rapidminer/resources/rapidminerrc.
Oct 28, 2011 9:30:55 AM com.rapidminer.PluginInitR initPlugin
INFO: Trying to load R Library...
Oct 28, 2011 9:30:55 AM org.rosuda.JRI.Rengine <clinit>
INFO: Creating Connection to R...
Oct 28, 2011 9:30:55 AM org.rosuda.JRI.Rengine loadLibrary
INFO: Trying to loaded R library from C:\Program Files\R\R-2.13.1\library\rJava\
jri\x64\jri.dll
Oct 28, 2011 9:30:55 AM org.rosuda.JRI.Rengine loadLibrary
INFO: Engine ID: class org.rosuda.JRI.Rengine ClassLoader:PluginClassLoader ([fi
le:/C:/Documents%20and%20Settings/swang8/.RapidMiner5/managed/rmx_r-5.1.4.jar])
Oct 28, 2011 9:30:55 AM org.rosuda.JRI.Rengine loadLibrary
INFO: Successfully loaded R library from C:\Program Files\R\R-2.13.1\library\rJa
va\jri\x64\jri.dll(true)
Oct 28, 2011 9:30:57 AM com.rapidminer.parameter.ParameterTypePassword decryptPa
ssword
WARNING: Password in XML file looks like unencrypted plain text.
I tried to get the R extension working for rapid miner and ran into some very odd issues. Basically my rapid miner starts up but the GUI never shows. I'm usiing the .bat shell program to start rapidminer and this is the output I see:
Note sure what's going on here. I'm pretty sure I have all my environmental variables and directories set correct as it seems to find the rapid miner libraries etc.
RAPIDMINER_HOME is not set. Trying the directory 'C:\Program Files\Rapid-I\Rapid
Miner5\scripts\..'...
Using local jre: C:\Program Files\Rapid-I\RapidMiner5\scripts\..\jre\bin\java.ex
e...
Starting RapidMiner from 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..' using
classes from 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..\lib\rapidminer.ja
r'...
Oct 28, 2011 9:30:45 AM com.rapid_i.Launcher ensureRapidMinerHomeSet
INFO: rapidminer.home is 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..'.
Oct 28, 2011 9:30:45 AM com.rapid_i.Launcher main
INFO: Launching RapidMiner, platform WIN64
Oct 28, 2011 9:30:46 AM com.rapid_i.Launcher ensureRapidMinerHomeSet
INFO: rapidminer.home is 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..'.
Oct 28, 2011 9:30:46 AM com.rapidminer.tools.ParameterService init
INFO: Reading configuration resource com/rapidminer/resources/rapidminerrc.
Oct 28, 2011 9:30:46 AM com.rapidminer.PluginInitR initPlugin
INFO: Trying to load R Library...
Oct 28, 2011 9:30:46 AM org.rosuda.JRI.Rengine <clinit>
INFO: Creating Connection to R...
Oct 28, 2011 9:30:46 AM org.rosuda.JRI.Rengine loadLibrary
INFO: Trying to loaded R library from C:\Program Files\R\R-2.13.1\library\rJava\
jri\x64\jri.dll
Oct 28, 2011 9:30:46 AM org.rosuda.JRI.Rengine loadLibrary
INFO: Engine ID: class org.rosuda.JRI.Rengine ClassLoader:PluginClassLoader ([fi
le:/C:/Documents%20and%20Settings/swang8/.RapidMiner5/managed/rmx_r-5.1.4.jar])
Oct 28, 2011 9:30:46 AM org.rosuda.JRI.Rengine loadLibrary
INFO: Successfully loaded R library from C:\Program Files\R\R-2.13.1\library\rJa
va\jri\x64\jri.dll(true)
Oct 28, 2011 9:30:48 AM com.rapidminer.parameter.ParameterTypePassword decryptPa
ssword
WARNING: Password in XML file looks like unencrypted plain text.
[Fatal Error] :1:1: Content is not allowed in prolog.
Oct 28, 2011 9:30:50 AM com.rapidminer.operator.r.ROperatorFactory readROperator
Fragments
WARNING: Could not read R fragments from 'file:/C:/Program%20Files/Rapid-I/Rapid
Miner5/scripts/', error: Content is not allowed in prolog.
org.xml.sax.SAXParseException: Content is not allowed in prolog.
at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown So
urce)
at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unk
nown Source)
at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
at com.rapidminer.io.process.XMLTools.parse(XMLTools.java:175)
at com.rapidminer.operator.r.ROperatorFactory.readROperatorFragments(ROp
eratorFactory.java:166)
at com.rapidminer.operator.r.ROperatorFactory.<init>(ROperatorFactory.ja
va:129)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Sou
rce)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at java.lang.Class.newInstance0(Unknown Source)
at java.lang.Class.newInstance(Unknown Source)
at com.rapidminer.tools.OperatorService.parseOperators(OperatorService.j
ava:294)
at com.rapidminer.tools.OperatorService.parseOperators(OperatorService.j
ava:232)
at com.rapidminer.tools.OperatorService.registerOperators(OperatorServic
e.java:206)
at com.rapidminer.tools.plugin.Plugin.registerOperators(Plugin.java:471)
at com.rapidminer.tools.plugin.Plugin.registerAllPluginOperators(Plugin.
java:725)
at com.rapidminer.tools.OperatorService.init(OperatorService.java:167)
at com.rapidminer.RapidMiner.init(RapidMiner.java:465)
at com.rapidminer.gui.RapidMinerGUI.run(RapidMinerGUI.java:221)
at com.rapidminer.gui.RapidMinerGUI.launch(RapidMinerGUI.java:505)
at com.rapidminer.gui.RapidMinerGUI.main(RapidMinerGUI.java:488)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.rapid_i.Launcher.main(Launcher.java:334)
[Fatal Error] :1:1: Content is not allowed in prolog.
Oct 28, 2011 9:30:50 AM 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.SAXParseExc
eption: Content is not allowed in prolog.
at com.rapidminer.tools.documentation.XMLOperatorDocBundle.<init>(XMLOpe
ratorDocBundle.java:119)
at com.rapidminer.operator.r.ROperatorFactory.<init>(ROperatorFactory.ja
va:150)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Sou
rce)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at java.lang.Class.newInstance0(Unknown Source)
at java.lang.Class.newInstance(Unknown Source)
at com.rapidminer.tools.OperatorService.parseOperators(OperatorService.j
ava:294)
at com.rapidminer.tools.OperatorService.parseOperators(OperatorService.j
ava:232)
at com.rapidminer.tools.OperatorService.registerOperators(OperatorServic
e.java:206)
at com.rapidminer.tools.plugin.Plugin.registerOperators(Plugin.java:471)
at com.rapidminer.tools.plugin.Plugin.registerAllPluginOperators(Plugin.
java:725)
at com.rapidminer.tools.OperatorService.init(OperatorService.java:167)
at com.rapidminer.RapidMiner.init(RapidMiner.java:465)
at com.rapidminer.gui.RapidMinerGUI.run(RapidMinerGUI.java:221)
at com.rapidminer.gui.RapidMinerGUI.launch(RapidMinerGUI.java:505)
at com.rapidminer.gui.RapidMinerGUI.main(RapidMinerGUI.java:488)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.rapid_i.Launcher.main(Launcher.java:334)
Caused by: org.xml.sax.SAXParseException: Content is not allowed in prolog.
at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown So
urce)
at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unk
nown Source)
at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
at com.rapidminer.tools.documentation.XMLOperatorDocBundle.<init>(XMLOpe
ratorDocBundle.java:117)
... 22 more
Oct 28, 2011 9:30:50 AM com.rapidminer.tools.plugin.Plugin registerOperators
INFO: No operator descriptor specified for plugin Community. Trying plugin initi
aliztation class com.rapidminer.community.CommunityPluginInit.
Oct 28, 2011 9:30:50 AM com.rapidminer.tools.plugin.Plugin registerOperators
WARNING: No operator descriptor defined for: Community
Oct 28, 2011 9:30:51 AM com.rapidminer.tools.jdbc.JDBCProperties <init>
WARNING: Missing database driver class name for 'ODBC Bridge (e.g. Access)'
Oct 28, 2011 9:30:51 AM com.rapidminer.tools.jdbc.JDBCProperties registerDrivers
INFO: JDBC driver ca.ingres.jdbc.IngresDriver not found. Probably the driver is
not installed.
Oct 28, 2011 9:30:51 AM com.rapidminer.tools.jdbc.JDBCProperties registerDrivers
INFO: JDBC driver oracle.jdbc.driver.OracleDriver not found. Probably the driver
is not installed.
initGui(MainFrame mainFrame)
Starting RapidMiner from 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..' using
classes from 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..\lib\rapidminer.ja
r'...
Oct 28, 2011 9:30:53 AM com.rapid_i.Launcher ensureRapidMinerHomeSet
INFO: rapidminer.home is 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..'.
Oct 28, 2011 9:30:53 AM com.rapid_i.Launcher main
INFO: Launching RapidMiner, platform WIN64
Oct 28, 2011 9:30:55 AM com.rapid_i.Launcher ensureRapidMinerHomeSet
INFO: rapidminer.home is 'C:\Program Files\Rapid-I\RapidMiner5\scripts\..'.
Oct 28, 2011 9:30:55 AM com.rapidminer.tools.ParameterService init
INFO: Reading configuration resource com/rapidminer/resources/rapidminerrc.
Oct 28, 2011 9:30:55 AM com.rapidminer.PluginInitR initPlugin
INFO: Trying to load R Library...
Oct 28, 2011 9:30:55 AM org.rosuda.JRI.Rengine <clinit>
INFO: Creating Connection to R...
Oct 28, 2011 9:30:55 AM org.rosuda.JRI.Rengine loadLibrary
INFO: Trying to loaded R library from C:\Program Files\R\R-2.13.1\library\rJava\
jri\x64\jri.dll
Oct 28, 2011 9:30:55 AM org.rosuda.JRI.Rengine loadLibrary
INFO: Engine ID: class org.rosuda.JRI.Rengine ClassLoader:PluginClassLoader ([fi
le:/C:/Documents%20and%20Settings/swang8/.RapidMiner5/managed/rmx_r-5.1.4.jar])
Oct 28, 2011 9:30:55 AM org.rosuda.JRI.Rengine loadLibrary
INFO: Successfully loaded R library from C:\Program Files\R\R-2.13.1\library\rJa
va\jri\x64\jri.dll(true)
Oct 28, 2011 9:30:57 AM com.rapidminer.parameter.ParameterTypePassword decryptPa
ssword
WARNING: Password in XML file looks like unencrypted plain text.
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