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BC 2.5/Vista - BC-R R does not start
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| !SESSION 2011-10-20 13:15:37.276 ----------------------------------------------- | |
| eclipse.buildId=2.5.0.201108060919 | |
| java.version=1.6.0_29 | |
| java.vendor=Sun Microsystems Inc. | |
| BootLoader constants: OS=win32, ARCH=x86, WS=win32, NL=en_US | |
| Framework arguments: -noupdate | |
| Command-line arguments: -os win32 -ws win32 -arch x86 -data @nodefault -noupdate -consolelog | |
| !ENTRY de.walware.rj.servi 4 0 2011-10-20 13:15:55.928 | |
| !MESSAGE An exception was thrown when trying to start the node (make a node). | |
| !STACK 0 | |
| de.walware.rj.RjException: Error starting R node: | |
| <COMMAND> | |
| C:\Program Files\Java\jre6\bin\java | |
| -classpath | |
| /C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/de.walware.rj.data_0.5.5.201107191712.jar;/C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar;/C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/de.walware.rj.servi_0.5.3.201107191712.jar;/C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/de.walware.rj.client_0.5.1.201107191712.jar;/C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/org.eclipse.equinox.common_3.6.0.v20100503.jar;/c:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/org.eclipse.osgi_3.6.2.R36x_v20110210.jar | |
| -Djava.security.policy=jar:file:/C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar!/localhost.policy | |
| -Djava.rmi.server.codebase=file:/C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar | |
| -Xss16384k | |
| de.walware.rj.servi.internal.NodeController | |
| rmi://127.0.0.1:53876/Rconsole-1319109353738 | |
| -verbose | |
| </COMMAND> | |
| <STDOUT> | |
| </STDOUT> | |
| <LOG file="out.log"> | |
| (RServi) R node log | |
| Oct 20, 2011 1:15:53 PM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose | |
| CONFIG: verbose mode enabled. | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose | |
| CONFIG: java properties: | |
| java.runtime.name=Java(TM) SE Runtime Environment | |
| sun.boot.library.path=C:\Program Files\Java\jre6\bin | |
| java.vm.version=20.4-b02 | |
| java.vm.vendor=Sun Microsystems Inc. | |
| java.vendor.url=http://java.sun.com/ | |
| path.separator=; | |
| java.vm.name=Java HotSpot(TM) Client VM | |
| file.encoding.pkg=sun.io | |
| sun.java.launcher=SUN_STANDARD | |
| user.country=US | |
| sun.os.patch.level=Service Pack 2 | |
| java.vm.specification.name=Java Virtual Machine Specification | |
| user.dir=C:\Users\ADMINI~1\AppData\Local\Temp\Rconsole-1319109353738 | |
| java.runtime.version=1.6.0_29-b11 | |
| java.awt.graphicsenv=sun.awt.Win32GraphicsEnvironment | |
| java.endorsed.dirs=C:\Program Files\Java\jre6\lib\endorsed | |
| os.arch=x86 | |
| java.io.tmpdir=C:\Users\ADMINI~1\AppData\Local\Temp\ | |
| line.separator= | |
| java.vm.specification.vendor=Sun Microsystems Inc. | |
| user.variant= | |
| os.name=Windows Vista | |
| sun.jnu.encoding=Cp1252 | |
| java.library.path=C:\Program Files\Java\jre6\bin;C:\Windows\Sun\Java\bin;C:\Windows\system32;C:\Windows;C:\Program Files\R\R-2.13.2\bin\i386;C:/Program Files/Java/jre6/bin/client;C:/Program Files/Java/jre6/bin;C:/Program Files/Java/jre6/lib/i386;C:\Program Files\Parallels\Parallels Tools\Applications;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Users\Administrator\Desktop\Bioclipse.2.5.0.win32.win32.x86;;. | |
| java.specification.name=Java Platform API Specification | |
| java.class.version=50.0 | |
| sun.management.compiler=HotSpot Client Compiler | |
| os.version=6.0 | |
| user.home=C:\Users\Administrator | |
| java.security.policy=jar:file:/C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar!/localhost.policy | |
| user.timezone=Europe/Berlin | |
| java.awt.printerjob=sun.awt.windows.WPrinterJob | |
| file.encoding=Cp1252 | |
| java.specification.version=1.6 | |
| java.class.path=/C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/de.walware.rj.data_0.5.5.201107191712.jar;/C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar;/C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/de.walware.rj.servi_0.5.3.201107191712.jar;/C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/de.walware.rj.client_0.5.1.201107191712.jar;/C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/org.eclipse.equinox.common_3.6.0.v20100503.jar;/c:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/org.eclipse.osgi_3.6.2.R36x_v20110210.jar | |
| user.name=Administrator | |
| java.vm.specification.version=1.0 | |
| sun.java.command=de.walware.rj.servi.internal.NodeController rmi://127.0.0.1:53876/Rconsole-1319109353738 -verbose | |
| java.home=C:\Program Files\Java\jre6 | |
| sun.arch.data.model=32 | |
| user.language=en | |
| java.specification.vendor=Sun Microsystems Inc. | |
| awt.toolkit=sun.awt.windows.WToolkit | |
| java.vm.info=mixed mode, sharing | |
| java.version=1.6.0_29 | |
| java.ext.dirs=C:\Program Files\Java\jre6\lib\ext;C:\Windows\Sun\Java\lib\ext | |
| sun.boot.class.path=C:\Program Files\Java\jre6\lib\resources.jar;C:\Program Files\Java\jre6\lib\rt.jar;C:\Program Files\Java\jre6\lib\sunrsasign.jar;C:\Program Files\Java\jre6\lib\jsse.jar;C:\Program Files\Java\jre6\lib\jce.jar;C:\Program Files\Java\jre6\lib\charsets.jar;C:\Program Files\Java\jre6\lib\modules\jdk.boot.jar;C:\Program Files\Java\jre6\classes | |
| java.vendor=Sun Microsystems Inc. | |
| file.separator=\ | |
| java.vendor.url.bug=http://java.sun.com/cgi-bin/bugreport.cgi | |
| sun.io.unicode.encoding=UnicodeLittle | |
| sun.cpu.endian=little | |
| sun.desktop=windows | |
| java.rmi.server.codebase=file:/C:/Users/Administrator/Desktop/Bioclipse.2.5.0.win32.win32.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar | |
| sun.cpu.isalist=pentium_pro+mmx pentium_pro pentium+mmx pentium i486 i386 i86 | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose | |
| CONFIG: env variables: | |
| USERPROFILE=C:\Users\Administrator | |
| ProgramData=C:\ProgramData | |
| PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC | |
| JAVA_HOME=C:\Program Files\Java\jre6 | |
| TRACE_FORMAT_SEARCH_PATH=\\winseqfe\release\Windows6.0\lh_sp2rtm\6002.18005.090410-1830\x86fre\symbols.pri\TraceFormat | |
| TEMP=C:\Users\ADMINI~1\AppData\Local\Temp | |
| SystemDrive=C: | |
| ProgramFiles=C:\Program Files | |
| HOMEDRIVE=C: | |
| PROCESSOR_REVISION=170a | |
| USERDOMAIN=MACMINI69E6 | |
| ALLUSERSPROFILE=C:\ProgramData | |
| DFSTRACINGON=FALSE | |
| PROCESSOR_IDENTIFIER=x86 Family 6 Model 23 Stepping 10, GenuineIntel | |
| SESSIONNAME=Console | |
| R_HOME=C:\Program Files\R\R-2.13.2 | |
| TMP=C:\Users\ADMINI~1\AppData\Local\Temp | |
| LOGONSERVER=\\MACMINI69E6 | |
| CommonProgramFiles=C:\Program Files\Common Files | |
| =::=::\ | |
| PROCESSOR_ARCHITECTURE=x86 | |
| FP_NO_HOST_CHECK=NO | |
| OS=Windows_NT | |
| PATH=C:\Program Files\R\R-2.13.2\bin\i386;C:/Program Files/Java/jre6/bin/client;C:/Program Files/Java/jre6/bin;C:/Program Files/Java/jre6/lib/i386;C:\Program Files\Parallels\Parallels Tools\Applications;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Users\Administrator\Desktop\Bioclipse.2.5.0.win32.win32.x86; | |
| HOMEPATH=\Users\Administrator | |
| PROCESSOR_LEVEL=6 | |
| LOCALAPPDATA=C:\Users\Administrator\AppData\Local | |
| COMPUTERNAME=MACMINI69E6 | |
| windir=C:\Windows | |
| SystemRoot=C:\Windows | |
| NUMBER_OF_PROCESSORS=1 | |
| USERNAME=Administrator | |
| PSModulePath=C:\Windows\system32\WindowsPowerShell\v1.0\Modules\ | |
| PUBLIC=C:\Users\Public | |
| R_ARCH=/i386 | |
| ComSpec=C:\Windows\system32\cmd.exe | |
| APPDATA=C:\Users\Administrator\AppData\Roaming | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.servi.internal.NodeController start | |
| INFO: [Control:Rconsole-1319109353738] Initializing R node... | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader <init> | |
| CONFIG: System URL classloader: enabled | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader <init> | |
| CONFIG: Alternative classloader: disabled | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader initRLibs | |
| CONFIG: JR library path: | |
| C:/Program Files/R/R-2.13.2/library | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added 'C:\Program Files\R\R-2.13.2\library\rJava\java' to classpath of URL loader | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader <init> | |
| CONFIG: registered JRI: C:\Program Files\R\R-2.13.2\library\rj\jri\i386\jri.dll | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added 'C:\Program Files\R\R-2.13.2\library\rj\jri\JRI.jar' to classpath of URL loader | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added 'C:\Program Files\R\R-2.13.2\library\rj\server\rj.jar' to classpath of URL loader | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added 'C:\Users\Administrator\Desktop\Bioclipse.2.5.0.win32.win32.x86\plugins\de.walware.rj.server_0.5.5.201107191712.jar' to classpath of URL loader | |
| Oct 20, 2011 1:15:54 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.REXP | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.REXP' using URL loader | |
| Oct 20, 2011 1:15:54 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.RMainLoopCallbacks | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.RMainLoopCallbacks' using URL loader | |
| Oct 20, 2011 1:15:54 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.Rengine | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.Rengine' using URL loader | |
| Oct 20, 2011 1:15:54 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.Mutex | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.Mutex' using URL loader | |
| Oct 20, 2011 1:15:54 PM RJavaClassLoader findLibrary | |
| FINER: ENTRY jri | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader findLibrary | |
| FINE: Mapping to C:\Program Files\R\R-2.13.2\library\rj\jri\i386\jri.dll | |
| Oct 20, 2011 1:15:54 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIServer | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIServer' using URL loader | |
| Oct 20, 2011 1:15:54 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIServer$InitCallbacks | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIServer$InitCallbacks' using URL loader | |
| Oct 20, 2011 1:15:54 PM RJavaClassLoader findLibrary | |
| FINER: ENTRY jri | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader findLibrary | |
| FINE: Mapping to C:\Program Files\R\R-2.13.2\library\rj\jri\i386\jri.dll | |
| Oct 20, 2011 1:15:54 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.RConfig | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.RConfig' using URL loader | |
| Oct 20, 2011 1:15:54 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIObjectFactory | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIObjectFactory' using URL loader | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.JRIServer initEngine | |
| FINER: Pointers: | |
| NULL = 0x22124a0 | |
| Unbound = 0x2212484 | |
| MissingArg = 0x2212468 | |
| BaseEnv = 0x8c5d70 | |
| AutoloadEnv = 0x152fa3c | |
| RJTempEnv = 0xef1f758 | |
| functionSymbol = 0x221d388 | |
| ifSymbol = 0x221d5d4 | |
| AssignSymbol = 0x221d334 | |
| xSymbol = 0x8c9a34 | |
| zSymbol = 0xaa7739c | |
| objectSymbol = 0xaa514b8 | |
| envSymbol = 0x8c8de8 | |
| nameSymbol = 0x2212158 | |
| realSymbol = 0x15181f0 | |
| imaginarySymbol = 0xef1fad8 | |
| newSymbol = 0xaa66dbc | |
| ClassSymbol = 0xef1fa68 | |
| exprSymbol = 0x8cdf88 | |
| errorSymbol = 0x2223ee0 | |
| factorClassString = 0xef1de70 | |
| orderedClassString = 0xef1de90 | |
| dataframeClassString = 0xef1de50 | |
| lengthFun = 0x3f09a0 | |
| complexFun = 0xef1f624 | |
| envNameFun = 0xef21054 | |
| headerFun = 0xef21ee8 | |
| s4classFun = 0xef21ba0 | |
| slotNamesFun = 0xef28990 | |
| ReFun = 0x3f43b4 | |
| ImFun = 0x3f4360 | |
| ItemFun = 0x221d104 | |
| tryCatchFun = 0x2227ee4 | |
| evalTryCatch_errorExpr = 0xef2aa80 | |
| evalTemp_classExpr = 0xef2a3a8 | |
| evalTemp_rmExpr = 0xef2a368 | |
| evalDummyExpr = 0xef2a2a8 | |
| Oct 20, 2011 1:15:54 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIVectorImpl | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIVectorImpl' using URL loader | |
| Oct 20, 2011 1:15:54 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRICharacterDataImpl | |
| Oct 20, 2011 1:15:54 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRICharacterDataImpl' using URL loader | |
| Oct 20, 2011 1:15:55 PM de.walware.rj.server.jri.JRIServer start | |
| INFO: R engine started successfully. New Client-State: 'Connected'. | |
| Oct 20, 2011 1:15:55 PM de.walware.rj.servi.internal.NodeServer start1 | |
| FINE: Initializing R node: Loading R package 'rj'... | |
| Oct 20, 2011 1:15:55 PM de.walware.rj.servi.internal.NodeServer start1 | |
| FINE: Initializing R node: Preparing R workspace for first client... | |
| Oct 20, 2011 1:15:55 PM de.walware.rj.servi.internal.NodeController start | |
| FINE: [Control:Rconsole-1319109353738] Initializing R node: R engine started and initialized. | |
| Oct 20, 2011 1:15:55 PM de.walware.rj.servi.internal.NodeController start | |
| FINE: [Control:Rconsole-1319109353738] Initializing R node: Publishing in registry... | |
| Oct 20, 2011 1:15:55 PM de.walware.rj.server.srvImpl.AbstractServerControl publishServer | |
| SEVERE: [Control:Rconsole-1319109353738] init server failed. | |
| java.rmi.ServerException: RemoteException occurred in server thread; nested exception is: | |
| java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is: | |
| java.lang.ClassNotFoundException: access to class loader denied | |
| at sun.rmi.server.UnicastServerRef.oldDispatch(Unknown Source) | |
| at sun.rmi.server.UnicastServerRef.dispatch(Unknown Source) | |
| at sun.rmi.transport.Transport$1.run(Unknown Source) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at sun.rmi.transport.Transport.serviceCall(Unknown Source) | |
| at sun.rmi.transport.tcp.TCPTransport.handleMessages(Unknown Source) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(Unknown Source) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(Unknown Source) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) | |
| at java.lang.Thread.run(Unknown Source) | |
| at sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(Unknown Source) | |
| at sun.rmi.transport.StreamRemoteCall.executeCall(Unknown Source) | |
| at sun.rmi.server.UnicastRef.invoke(Unknown Source) | |
| at sun.rmi.registry.RegistryImpl_Stub.bind(Unknown Source) | |
| at java.rmi.Naming.bind(Unknown Source) | |
| at de.walware.rj.server.srvImpl.AbstractServerControl.publishServer(AbstractServerControl.java:187) | |
| at de.walware.rj.servi.internal.NodeController.start(NodeController.java:75) | |
| at de.walware.rj.servi.internal.NodeController.main(NodeController.java:48) | |
| Caused by: java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is: | |
| java.lang.ClassNotFoundException: access to class loader denied | |
| at sun.rmi.registry.RegistryImpl_Skel.dispatch(Unknown Source) | |
| at sun.rmi.server.UnicastServerRef.oldDispatch(Unknown Source) | |
| at sun.rmi.server.UnicastServerRef.dispatch(Unknown Source) | |
| at sun.rmi.transport.Transport$1.run(Unknown Source) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at sun.rmi.transport.Transport.serviceCall(Unknown Source) | |
| at sun.rmi.transport.tcp.TCPTransport.handleMessages(Unknown Source) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(Unknown Source) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(Unknown Source) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) | |
| at java.lang.Thread.run(Unknown Source) | |
| Caused by: java.lang.ClassNotFoundException: access to class loader denied | |
| at sun.rmi.server.LoaderHandler.loadProxyClass(Unknown Source) | |
| at java.rmi.server.RMIClassLoader$2.loadProxyClass(Unknown Source) | |
| at java.rmi.server.RMIClassLoader.loadProxyClass(Unknown Source) | |
| at sun.rmi.server.MarshalInputStream.resolveProxyClass(Unknown Source) | |
| at java.io.ObjectInputStream.readProxyDesc(Unknown Source) | |
| at java.io.ObjectInputStream.readClassDesc(Unknown Source) | |
| at java.io.ObjectInputStream.readOrdinaryObject(Unknown Source) | |
| at java.io.ObjectInputStream.readObject0(Unknown Source) | |
| at java.io.ObjectInputStream.readObject(Unknown Source) | |
| ... 12 more | |
| Caused by: java.security.AccessControlException: access denied (java.io.FilePermission \C:\Users\Administrator\Desktop\Bioclipse.2.5.0.win32.win32.x86\plugins\- read) | |
| at java.security.AccessControlContext.checkPermission(Unknown Source) | |
| at java.security.AccessController.checkPermission(Unknown Source) | |
| at java.lang.SecurityManager.checkPermission(Unknown Source) | |
| at sun.rmi.server.LoaderHandler$Loader.checkPermissions(Unknown Source) | |
| at sun.rmi.server.LoaderHandler$Loader.access$000(Unknown Source) | |
| ... 21 more | |
| Oct 20, 2011 1:15:55 PM de.walware.rj.server.srvImpl.AbstractServerControl checkCleanup | |
| INFO: [Control:Rconsole-1319109353738] cleaning up server resources... | |
| </LOG> | |
| -------- | |
| at de.walware.rj.servi.internal.LocalNodeFactory.createNode(LocalNodeFactory.java:473) | |
| at de.walware.rj.servi.internal.EmbeddedManager.start(EmbeddedManager.java:83) | |
| at net.bioclipse.r.RServiManager.startEmbedded(RServiManager.java:177) | |
| at net.bioclipse.r.RServiManager.setEmbedded(RServiManager.java:119) | |
| at net.bioclipse.r.business.RBusinessManager.<init>(RBusinessManager.java:89) | |
| at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) | |
| at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) | |
| at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) | |
| at java.lang.reflect.Constructor.newInstance(Unknown Source) | |
| at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:83) | |
| at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:61) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:807) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:769) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:412) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:383) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:353) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:245) | |
| at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:169) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:242) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164) | |
| at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:269) | |
| at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:104) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1172) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:940) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:437) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:383) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:353) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:245) | |
| at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:169) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:242) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.isSingleton(AbstractBeanFactory.java:348) | |
| at org.springframework.osgi.service.exporter.support.OsgiServiceFactoryBean.afterPropertiesSet(OsgiServiceFactoryBean.java:179) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1288) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1257) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:438) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:383) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:353) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:245) | |
| at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:169) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:242) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164) | |
| at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:394) | |
| at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:736) | |
| at org.springframework.osgi.context.support.AbstractDelegatedExecutionApplicationContext.completeRefresh(AbstractDelegatedExecutionApplicationContext.java:251) | |
| at org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$CompleteRefreshTask.run(DependencyWaiterApplicationContextExecutor.java:136) | |
| at java.lang.Thread.run(Unknown Source) | |
| Caused by: de.walware.rj.RjException: R node process stopped (exit code = 156). | |
| at de.walware.rj.servi.internal.LocalNodeFactory.createNode(LocalNodeFactory.java:393) | |
| ... 49 more | |
| !SESSION 2011-10-20 13:55:57.762 ----------------------------------------------- | |
| eclipse.buildId=2.5.0.201108060919 | |
| java.version=1.6.0_29 | |
| java.vendor=Sun Microsystems Inc. | |
| BootLoader constants: OS=win32, ARCH=x86, WS=win32, NL=en_US | |
| Framework arguments: -noupdate | |
| Command-line arguments: -os win32 -ws win32 -arch x86 -data @nodefault -noupdate -consolelog | |
| !ENTRY org.eclipse.core.resources 2 10035 2011-10-20 13:56:03.282 | |
| !MESSAGE The workspace exited with unsaved changes in the previous session; refreshing workspace to recover changes. | |
| !SESSION 2011-10-20 13:57:45.113 ----------------------------------------------- | |
| eclipse.buildId=2.5.0.201108060919 | |
| java.version=1.6.0_29 | |
| java.vendor=Sun Microsystems Inc. | |
| BootLoader constants: OS=win32, ARCH=x86, WS=win32, NL=en_US | |
| Framework arguments: -noupdate | |
| Command-line arguments: -os win32 -ws win32 -arch x86 -data @nodefault -noupdate -consolelog | |
| !ENTRY org.eclipse.core.resources 2 10035 2011-10-20 13:57:50.051 | |
| !MESSAGE The workspace exited with unsaved changes in the previous session; refreshing workspace to recover changes. | |
| !ENTRY de.walware.rj.servi 4 0 2011-10-20 13:58:01.917 | |
| !MESSAGE An exception was thrown when trying to start the node (make a node). | |
| !STACK 0 | |
| de.walware.rj.RjException: Error starting R node: | |
| <COMMAND> | |
| C:\Program Files\Java\jre6\bin\java | |
| -classpath | |
| /C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/de.walware.rj.data_0.5.5.201107191712.jar;/C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/de.walware.rj.server_0.5.5.201107191712.jar;/C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/de.walware.rj.servi_0.5.3.201107191712.jar;/C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/de.walware.rj.client_0.5.1.201107191712.jar;/C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/org.eclipse.equinox.common_3.6.0.v20100503.jar;/c:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/org.eclipse.osgi_3.6.2.R36x_v20110210.jar | |
| -Djava.security.policy=jar:file:/C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/de.walware.rj.server_0.5.5.201107191712.jar!/localhost.policy | |
| -Djava.rmi.server.codebase=file:/C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/de.walware.rj.server_0.5.5.201107191712.jar | |
| -Xss16384k | |
| de.walware.rj.servi.internal.NodeController | |
| rmi://127.0.0.1:63860/Rconsole-1319111880617 | |
| -verbose | |
| </COMMAND> | |
| <STDOUT> | |
| </STDOUT> | |
| <LOG file="out.log"> | |
| (RServi) R node log | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose | |
| CONFIG: verbose mode enabled. | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose | |
| CONFIG: java properties: | |
| java.runtime.name=Java(TM) SE Runtime Environment | |
| sun.boot.library.path=C:\Program Files\Java\jre6\bin | |
| java.vm.version=20.4-b02 | |
| java.vm.vendor=Sun Microsystems Inc. | |
| java.vendor.url=http://java.sun.com/ | |
| path.separator=; | |
| java.vm.name=Java HotSpot(TM) Client VM | |
| file.encoding.pkg=sun.io | |
| sun.java.launcher=SUN_STANDARD | |
| user.country=US | |
| sun.os.patch.level=Service Pack 2 | |
| java.vm.specification.name=Java Virtual Machine Specification | |
| user.dir=C:\Users\ADMINI~1\AppData\Local\Temp\Rconsole-1319111880617 | |
| java.runtime.version=1.6.0_29-b11 | |
| java.awt.graphicsenv=sun.awt.Win32GraphicsEnvironment | |
| java.endorsed.dirs=C:\Program Files\Java\jre6\lib\endorsed | |
| os.arch=x86 | |
| java.io.tmpdir=C:\Users\ADMINI~1\AppData\Local\Temp\ | |
| line.separator= | |
| java.vm.specification.vendor=Sun Microsystems Inc. | |
| user.variant= | |
| os.name=Windows Vista | |
| sun.jnu.encoding=Cp1252 | |
| java.library.path=C:\Program Files\Java\jre6\bin;C:\Windows\Sun\Java\bin;C:\Windows\system32;C:\Windows;C:\Program Files\R\R-2.13.2\bin\i386;C:/Program Files/Java/jre6/bin/client;C:/Program Files/Java/jre6/bin;C:/Program Files/Java/jre6/lib/i386;C:\Program Files\Parallels\Parallels Tools\Applications;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Users\Administrator\Documents\Bioclipse.2.5.0;;. | |
| java.specification.name=Java Platform API Specification | |
| java.class.version=50.0 | |
| sun.management.compiler=HotSpot Client Compiler | |
| os.version=6.0 | |
| user.home=C:\Users\Administrator | |
| java.security.policy=jar:file:/C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/de.walware.rj.server_0.5.5.201107191712.jar!/localhost.policy | |
| user.timezone=Europe/Berlin | |
| java.awt.printerjob=sun.awt.windows.WPrinterJob | |
| file.encoding=Cp1252 | |
| java.specification.version=1.6 | |
| java.class.path=/C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/de.walware.rj.data_0.5.5.201107191712.jar;/C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/de.walware.rj.server_0.5.5.201107191712.jar;/C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/de.walware.rj.servi_0.5.3.201107191712.jar;/C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/de.walware.rj.client_0.5.1.201107191712.jar;/C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/org.eclipse.equinox.common_3.6.0.v20100503.jar;/c:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/org.eclipse.osgi_3.6.2.R36x_v20110210.jar | |
| user.name=Administrator | |
| java.vm.specification.version=1.0 | |
| sun.java.command=de.walware.rj.servi.internal.NodeController rmi://127.0.0.1:63860/Rconsole-1319111880617 -verbose | |
| java.home=C:\Program Files\Java\jre6 | |
| sun.arch.data.model=32 | |
| user.language=en | |
| java.specification.vendor=Sun Microsystems Inc. | |
| awt.toolkit=sun.awt.windows.WToolkit | |
| java.vm.info=mixed mode, sharing | |
| java.version=1.6.0_29 | |
| java.ext.dirs=C:\Program Files\Java\jre6\lib\ext;C:\Windows\Sun\Java\lib\ext | |
| sun.boot.class.path=C:\Program Files\Java\jre6\lib\resources.jar;C:\Program Files\Java\jre6\lib\rt.jar;C:\Program Files\Java\jre6\lib\sunrsasign.jar;C:\Program Files\Java\jre6\lib\jsse.jar;C:\Program Files\Java\jre6\lib\jce.jar;C:\Program Files\Java\jre6\lib\charsets.jar;C:\Program Files\Java\jre6\lib\modules\jdk.boot.jar;C:\Program Files\Java\jre6\classes | |
| java.vendor=Sun Microsystems Inc. | |
| file.separator=\ | |
| java.vendor.url.bug=http://java.sun.com/cgi-bin/bugreport.cgi | |
| sun.io.unicode.encoding=UnicodeLittle | |
| sun.cpu.endian=little | |
| sun.desktop=windows | |
| java.rmi.server.codebase=file:/C:/Users/Administrator/Documents/Bioclipse.2.5.0/plugins/de.walware.rj.server_0.5.5.201107191712.jar | |
| sun.cpu.isalist=pentium_pro+mmx pentium_pro pentium+mmx pentium i486 i386 i86 | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose | |
| CONFIG: env variables: | |
| USERPROFILE=C:\Users\Administrator | |
| ProgramData=C:\ProgramData | |
| PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC | |
| JAVA_HOME=C:\Program Files\Java\jre6 | |
| TRACE_FORMAT_SEARCH_PATH=\\winseqfe\release\Windows6.0\lh_sp2rtm\6002.18005.090410-1830\x86fre\symbols.pri\TraceFormat | |
| TEMP=C:\Users\ADMINI~1\AppData\Local\Temp | |
| SystemDrive=C: | |
| ProgramFiles=C:\Program Files | |
| HOMEDRIVE=C: | |
| PROCESSOR_REVISION=170a | |
| USERDOMAIN=MACMINI69E6 | |
| ALLUSERSPROFILE=C:\ProgramData | |
| DFSTRACINGON=FALSE | |
| PROCESSOR_IDENTIFIER=x86 Family 6 Model 23 Stepping 10, GenuineIntel | |
| SESSIONNAME=Console | |
| R_HOME=C:\Program Files\R\R-2.13.2 | |
| TMP=C:\Users\ADMINI~1\AppData\Local\Temp | |
| LOGONSERVER=\\MACMINI69E6 | |
| CommonProgramFiles=C:\Program Files\Common Files | |
| =::=::\ | |
| PROCESSOR_ARCHITECTURE=x86 | |
| FP_NO_HOST_CHECK=NO | |
| OS=Windows_NT | |
| PATH=C:\Program Files\R\R-2.13.2\bin\i386;C:/Program Files/Java/jre6/bin/client;C:/Program Files/Java/jre6/bin;C:/Program Files/Java/jre6/lib/i386;C:\Program Files\Parallels\Parallels Tools\Applications;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Users\Administrator\Documents\Bioclipse.2.5.0; | |
| HOMEPATH=\Users\Administrator | |
| PROCESSOR_LEVEL=6 | |
| LOCALAPPDATA=C:\Users\Administrator\AppData\Local | |
| COMPUTERNAME=MACMINI69E6 | |
| windir=C:\Windows | |
| SystemRoot=C:\Windows | |
| NUMBER_OF_PROCESSORS=1 | |
| USERNAME=Administrator | |
| PSModulePath=C:\Windows\system32\WindowsPowerShell\v1.0\Modules\ | |
| PUBLIC=C:\Users\Public | |
| R_ARCH=/i386 | |
| ComSpec=C:\Windows\system32\cmd.exe | |
| APPDATA=C:\Users\Administrator\AppData\Roaming | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.servi.internal.NodeController start | |
| INFO: [Control:Rconsole-1319111880617] Initializing R node... | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader <init> | |
| CONFIG: System URL classloader: enabled | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader <init> | |
| CONFIG: Alternative classloader: disabled | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader initRLibs | |
| CONFIG: JR library path: | |
| C:/Program Files/R/R-2.13.2/library | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added 'C:\Program Files\R\R-2.13.2\library\rJava\java' to classpath of URL loader | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader <init> | |
| CONFIG: registered JRI: C:\Program Files\R\R-2.13.2\library\rj\jri\i386\jri.dll | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added 'C:\Program Files\R\R-2.13.2\library\rj\jri\JRI.jar' to classpath of URL loader | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added 'C:\Program Files\R\R-2.13.2\library\rj\server\rj.jar' to classpath of URL loader | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added 'C:\Users\Administrator\Documents\Bioclipse.2.5.0\plugins\de.walware.rj.server_0.5.5.201107191712.jar' to classpath of URL loader | |
| Oct 20, 2011 1:58:00 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.REXP | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.REXP' using URL loader | |
| Oct 20, 2011 1:58:00 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.RMainLoopCallbacks | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.RMainLoopCallbacks' using URL loader | |
| Oct 20, 2011 1:58:00 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.Rengine | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.Rengine' using URL loader | |
| Oct 20, 2011 1:58:00 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.Mutex | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.Mutex' using URL loader | |
| Oct 20, 2011 1:58:00 PM RJavaClassLoader findLibrary | |
| FINER: ENTRY jri | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader findLibrary | |
| FINE: Mapping to C:\Program Files\R\R-2.13.2\library\rj\jri\i386\jri.dll | |
| Oct 20, 2011 1:58:00 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIServer | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIServer' using URL loader | |
| Oct 20, 2011 1:58:00 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIServer$InitCallbacks | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIServer$InitCallbacks' using URL loader | |
| Oct 20, 2011 1:58:00 PM RJavaClassLoader findLibrary | |
| FINER: ENTRY jri | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader findLibrary | |
| FINE: Mapping to C:\Program Files\R\R-2.13.2\library\rj\jri\i386\jri.dll | |
| Oct 20, 2011 1:58:00 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.RConfig | |
| Oct 20, 2011 1:58:00 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.RConfig' using URL loader | |
| Oct 20, 2011 1:58:01 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIObjectFactory | |
| Oct 20, 2011 1:58:01 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIObjectFactory' using URL loader | |
| Oct 20, 2011 1:58:01 PM de.walware.rj.server.jri.JRIServer initEngine | |
| FINER: Pointers: | |
| NULL = 0xa9e24a0 | |
| Unbound = 0xa9e2484 | |
| MissingArg = 0xa9e2468 | |
| BaseEnv = 0x20d5d70 | |
| AutoloadEnv = 0xa9ff69c | |
| RJTempEnv = 0xef1f308 | |
| functionSymbol = 0xa9ed388 | |
| ifSymbol = 0xa9ed5d4 | |
| AssignSymbol = 0xa9ed334 | |
| xSymbol = 0x20d9a34 | |
| zSymbol = 0xea97104 | |
| objectSymbol = 0xaa31118 | |
| envSymbol = 0x20d8de8 | |
| nameSymbol = 0xa9e2158 | |
| realSymbol = 0xa997a20 | |
| imaginarySymbol = 0xef1f688 | |
| newSymbol = 0xaa46afc | |
| ClassSymbol = 0xef1f618 | |
| exprSymbol = 0x20ddf88 | |
| errorSymbol = 0xaa03c90 | |
| factorClassString = 0xef1da20 | |
| orderedClassString = 0xef1da40 | |
| dataframeClassString = 0xef1da00 | |
| lengthFun = 0x3f09a0 | |
| complexFun = 0xef1f1d4 | |
| envNameFun = 0xef20c04 | |
| headerFun = 0xef21a98 | |
| s4classFun = 0xef21750 | |
| slotNamesFun = 0xef28540 | |
| ReFun = 0x3f43b4 | |
| ImFun = 0x3f4360 | |
| ItemFun = 0xa9ed104 | |
| tryCatchFun = 0xaa07c94 | |
| evalTryCatch_errorExpr = 0xef2a630 | |
| evalTemp_classExpr = 0xef29f58 | |
| evalTemp_rmExpr = 0xef29f18 | |
| evalDummyExpr = 0xef29e58 | |
| Oct 20, 2011 1:58:01 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIVectorImpl | |
| Oct 20, 2011 1:58:01 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIVectorImpl' using URL loader | |
| Oct 20, 2011 1:58:01 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRICharacterDataImpl | |
| Oct 20, 2011 1:58:01 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRICharacterDataImpl' using URL loader | |
| Oct 20, 2011 1:58:01 PM de.walware.rj.server.jri.JRIServer start | |
| INFO: R engine started successfully. New Client-State: 'Connected'. | |
| Oct 20, 2011 1:58:01 PM de.walware.rj.servi.internal.NodeServer start1 | |
| FINE: Initializing R node: Loading R package 'rj'... | |
| Oct 20, 2011 1:58:01 PM de.walware.rj.servi.internal.NodeServer start1 | |
| FINE: Initializing R node: Preparing R workspace for first client... | |
| Oct 20, 2011 1:58:01 PM de.walware.rj.servi.internal.NodeController start | |
| FINE: [Control:Rconsole-1319111880617] Initializing R node: R engine started and initialized. | |
| Oct 20, 2011 1:58:01 PM de.walware.rj.servi.internal.NodeController start | |
| FINE: [Control:Rconsole-1319111880617] Initializing R node: Publishing in registry... | |
| Oct 20, 2011 1:58:01 PM de.walware.rj.server.srvImpl.AbstractServerControl publishServer | |
| SEVERE: [Control:Rconsole-1319111880617] init server failed. | |
| java.rmi.ServerException: RemoteException occurred in server thread; nested exception is: | |
| java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is: | |
| java.lang.ClassNotFoundException: access to class loader denied | |
| at sun.rmi.server.UnicastServerRef.oldDispatch(Unknown Source) | |
| at sun.rmi.server.UnicastServerRef.dispatch(Unknown Source) | |
| at sun.rmi.transport.Transport$1.run(Unknown Source) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at sun.rmi.transport.Transport.serviceCall(Unknown Source) | |
| at sun.rmi.transport.tcp.TCPTransport.handleMessages(Unknown Source) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(Unknown Source) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(Unknown Source) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) | |
| at java.lang.Thread.run(Unknown Source) | |
| at sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(Unknown Source) | |
| at sun.rmi.transport.StreamRemoteCall.executeCall(Unknown Source) | |
| at sun.rmi.server.UnicastRef.invoke(Unknown Source) | |
| at sun.rmi.registry.RegistryImpl_Stub.bind(Unknown Source) | |
| at java.rmi.Naming.bind(Unknown Source) | |
| at de.walware.rj.server.srvImpl.AbstractServerControl.publishServer(AbstractServerControl.java:187) | |
| at de.walware.rj.servi.internal.NodeController.start(NodeController.java:75) | |
| at de.walware.rj.servi.internal.NodeController.main(NodeController.java:48) | |
| Caused by: java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is: | |
| java.lang.ClassNotFoundException: access to class loader denied | |
| at sun.rmi.registry.RegistryImpl_Skel.dispatch(Unknown Source) | |
| at sun.rmi.server.UnicastServerRef.oldDispatch(Unknown Source) | |
| at sun.rmi.server.UnicastServerRef.dispatch(Unknown Source) | |
| at sun.rmi.transport.Transport$1.run(Unknown Source) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at sun.rmi.transport.Transport.serviceCall(Unknown Source) | |
| at sun.rmi.transport.tcp.TCPTransport.handleMessages(Unknown Source) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(Unknown Source) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(Unknown Source) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) | |
| at java.lang.Thread.run(Unknown Source) | |
| Caused by: java.lang.ClassNotFoundException: access to class loader denied | |
| at sun.rmi.server.LoaderHandler.loadProxyClass(Unknown Source) | |
| at java.rmi.server.RMIClassLoader$2.loadProxyClass(Unknown Source) | |
| at java.rmi.server.RMIClassLoader.loadProxyClass(Unknown Source) | |
| at sun.rmi.server.MarshalInputStream.resolveProxyClass(Unknown Source) | |
| at java.io.ObjectInputStream.readProxyDesc(Unknown Source) | |
| at java.io.ObjectInputStream.readClassDesc(Unknown Source) | |
| at java.io.ObjectInputStream.readOrdinaryObject(Unknown Source) | |
| at java.io.ObjectInputStream.readObject0(Unknown Source) | |
| at java.io.ObjectInputStream.readObject(Unknown Source) | |
| ... 12 more | |
| Caused by: java.security.AccessControlException: access denied (java.io.FilePermission \C:\Users\Administrator\Documents\Bioclipse.2.5.0\plugins\- read) | |
| at java.security.AccessControlContext.checkPermission(Unknown Source) | |
| at java.security.AccessController.checkPermission(Unknown Source) | |
| at java.lang.SecurityManager.checkPermission(Unknown Source) | |
| at sun.rmi.server.LoaderHandler$Loader.checkPermissions(Unknown Source) | |
| at sun.rmi.server.LoaderHandler$Loader.access$000(Unknown Source) | |
| ... 21 more | |
| Oct 20, 2011 1:58:01 PM de.walware.rj.server.srvImpl.AbstractServerControl checkCleanup | |
| INFO: [Control:Rconsole-1319111880617] cleaning up server resources... | |
| </LOG> | |
| -------- | |
| at de.walware.rj.servi.internal.LocalNodeFactory.createNode(LocalNodeFactory.java:473) | |
| at de.walware.rj.servi.internal.EmbeddedManager.start(EmbeddedManager.java:83) | |
| at net.bioclipse.r.RServiManager.startEmbedded(RServiManager.java:177) | |
| at net.bioclipse.r.RServiManager.setEmbedded(RServiManager.java:119) | |
| at net.bioclipse.r.business.RBusinessManager.<init>(RBusinessManager.java:89) | |
| at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) | |
| at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) | |
| at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) | |
| at java.lang.reflect.Constructor.newInstance(Unknown Source) | |
| at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:83) | |
| at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:61) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:807) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:769) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:412) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:383) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:353) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:245) | |
| at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:169) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:242) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164) | |
| at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:269) | |
| at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:104) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1172) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:940) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:437) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:383) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:353) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:245) | |
| at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:169) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:242) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.isSingleton(AbstractBeanFactory.java:348) | |
| at org.springframework.osgi.service.exporter.support.OsgiServiceFactoryBean.afterPropertiesSet(OsgiServiceFactoryBean.java:179) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1288) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1257) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:438) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:383) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:353) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:245) | |
| at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:169) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:242) | |
| at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164) | |
| at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:394) | |
| at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:736) | |
| at org.springframework.osgi.context.support.AbstractDelegatedExecutionApplicationContext.completeRefresh(AbstractDelegatedExecutionApplicationContext.java:251) | |
| at org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$CompleteRefreshTask.run(DependencyWaiterApplicationContextExecutor.java:136) | |
| at java.lang.Thread.run(Unknown Source) | |
| Caused by: de.walware.rj.RjException: R node process stopped (exit code = 156). | |
| at de.walware.rj.servi.internal.LocalNodeFactory.createNode(LocalNodeFactory.java:393) | |
| ... 49 more |
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