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| !SESSION 2011-11-14 15:15:34.901 ----------------------------------------------- | |
| eclipse.buildId=2.5.0.201108060919 | |
| java.version=1.6.0_22 | |
| java.vendor=Sun Microsystems Inc. | |
| BootLoader constants: OS=linux, ARCH=x86, WS=gtk, NL=en_US | |
| Framework arguments: -noupdate | |
| Command-line arguments: -os linux -ws gtk -arch x86 -data @nodefault -noupdate -consolelog | |
| !ENTRY org.eclipse.core.resources 2 10035 2011-11-14 15:15:36.356 | |
| !MESSAGE The workspace exited with unsaved changes in the previous session; refreshing workspace to recover changes. | |
| !ENTRY de.walware.rj.servi 4 0 2011-11-14 15:15:41.493 | |
| !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> | |
| /usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/bin/java | |
| -classpath | |
| /home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.data_0.5.5.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.servi_0.5.3.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.client_0.5.1.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/org.eclipse.equinox.common_3.6.0.v20100503.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/org.eclipse.osgi_3.6.2.R36x_v20110210.jar | |
| -Djava.security.policy=jar:file:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar!/localhost.policy | |
| -Djava.rmi.server.codebase=file:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar | |
| -Xss16384k | |
| de.walware.rj.servi.internal.NodeController | |
| rmi://127.0.0.1:59401/Rconsole-1321280140197 | |
| -verbose | |
| </COMMAND> | |
| <STDOUT> | |
| </STDOUT> | |
| <LOG file="out.log"> | |
| (RServi) R node log | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose | |
| CONFIG: verbose mode enabled. | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose | |
| CONFIG: java properties: | |
| java.runtime.name=OpenJDK Runtime Environment | |
| sun.boot.library.path=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386 | |
| java.vm.version=20.0-b11 | |
| java.vm.vendor=Sun Microsystems Inc. | |
| java.vendor.url=http://java.sun.com/ | |
| path.separator=: | |
| java.vm.name=OpenJDK Client VM | |
| file.encoding.pkg=sun.io | |
| sun.java.launcher=SUN_STANDARD | |
| user.country=US | |
| sun.os.patch.level=unknown | |
| java.vm.specification.name=Java Virtual Machine Specification | |
| user.dir=/tmp/Rconsole-1321280140197 | |
| java.runtime.version=1.6.0_22-b22 | |
| java.awt.graphicsenv=sun.awt.X11GraphicsEnvironment | |
| java.endorsed.dirs=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/endorsed | |
| os.arch=i386 | |
| java.io.tmpdir=/tmp | |
| line.separator= | |
| java.vm.specification.vendor=Sun Microsystems Inc. | |
| os.name=Linux | |
| sun.jnu.encoding=UTF-8 | |
| java.library.path=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386/client:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../lib/i386:/usr/lib/R/lib:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386/client:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386::/usr/java/packages/lib/i386:/lib:/usr/lib | |
| java.specification.name=Java Platform API Specification | |
| java.class.version=50.0 | |
| sun.management.compiler=HotSpot Client Compiler | |
| os.version=2.6.37.6-0.7-desktop | |
| user.home=/home/valyo | |
| java.security.policy=jar:file:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar!/localhost.policy | |
| user.timezone=Europe/Stockholm | |
| java.awt.printerjob=sun.print.PSPrinterJob | |
| file.encoding=UTF-8 | |
| java.specification.version=1.6 | |
| java.class.path=/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.data_0.5.5.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.servi_0.5.3.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.client_0.5.1.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/org.eclipse.equinox.common_3.6.0.v20100503.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/org.eclipse.osgi_3.6.2.R36x_v20110210.jar | |
| user.name=valyo | |
| java.vm.specification.version=1.0 | |
| sun.java.command=de.walware.rj.servi.internal.NodeController rmi://127.0.0.1:59401/Rconsole-1321280140197 -verbose | |
| java.home=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre | |
| sun.arch.data.model=32 | |
| user.language=en | |
| java.specification.vendor=Sun Microsystems Inc. | |
| java.vm.info=mixed mode | |
| java.version=1.6.0_22 | |
| java.ext.dirs=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/ext:/usr/java/packages/lib/ext | |
| sun.boot.class.path=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/resources.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/rt.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/sunrsasign.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/jsse.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/jce.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/charsets.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/netx.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/plugin.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/rhino.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/modules/jdk.boot.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/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=gnome | |
| java.rmi.server.codebase=file:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar | |
| sun.cpu.isalist= | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose | |
| CONFIG: env variables: | |
| TERM=xterm | |
| WINDOWMANAGER=/usr/bin/gnome | |
| JAVA_HOME=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre | |
| LESSCLOSE=lessclose.sh %s %s | |
| SESSION_MANAGER=local/linux-gwrj:@/tmp/.ICE-unix/2088,unix/linux-gwrj:/tmp/.ICE-unix/2088 | |
| GNOME_DESKTOP_SESSION_ID=this-is-deprecated | |
| HOSTTYPE=i386 | |
| R_LIBS_USER=/home/valyo/R/i686-suse-linux-gnu-library/2.13 | |
| MAIL=/var/spool/mail/valyo | |
| GDMSESSION=gnome | |
| XDG_SESSION_COOKIE=7dd418d636a94d6051b870050000045b-1321276104.432314-918606885 | |
| PWD=/home/valyo | |
| HOST=linux-gwrj | |
| HOSTNAME=linux-gwrj | |
| XCURSOR_THEME=DMZ | |
| XAUTHLOCALHOSTNAME=localhost | |
| GTK_IM_MODULE=cedilla | |
| G_FILENAME_ENCODING=@locale,UTF-8,ISO-8859-15,CP1252 | |
| G_BROKEN_FILENAMES=1 | |
| MACHTYPE=i686-suse-linux | |
| QT_SYSTEM_DIR=/usr/share/desktop-data | |
| NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat | |
| XDG_MENU_PREFIX=gnome- | |
| GDM_KEYBOARD_LAYOUT=us | |
| INPUTRC=/home/valyo/.inputrc | |
| TMPDIR=/tmp | |
| HISTSIZE=1000 | |
| XKEYSYMDB=/usr/X11R6/lib/X11/XKeysymDB | |
| PATH=/usr/lib/R/bin:/home/valyo/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games | |
| XDG_CONFIG_DIRS=/etc/xdg | |
| XNLSPATH=/usr/share/X11/nls | |
| LESS_ADVANCED_PREPROCESSOR=no | |
| LESS=-M -I -R | |
| PAGER=less | |
| PYTHONSTARTUP=/etc/pythonstart | |
| XAUTHORITY=/var/run/gdm/auth-for-valyo-fFNmlg/database | |
| GDM_LANG=en_US.utf8 | |
| SDK_HOME=/usr/lib/jvm/java | |
| WINDOWPATH=7 | |
| ALSA_CONFIG_PATH=/etc/alsa-pulse.conf | |
| USERNAME=valyo | |
| JAVA_ROOT=/usr/lib/jvm/java | |
| OSTYPE=linux | |
| LESSKEY=/etc/lesskey.bin | |
| GNOME_KEYRING_CONTROL=/tmp/keyring-nLLOmx | |
| SHLVL=0 | |
| MOZILLA_FIVE_HOME=/usr/lib/xulrunner-2.0.1 | |
| XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt | |
| MINICOM=-c on | |
| MANPATH=/usr/local/man:/usr/share/man | |
| COLORTERM=1 | |
| CPU=i686 | |
| QT_IM_SWITCHER=imsw-multi | |
| ICEAUTHORITY=/home/valyo/.ICEauthority | |
| XDG_DATA_DIRS=/usr/share | |
| NNTPSERVER=news | |
| QT_IM_MODULE=xim | |
| JDK_HOME=/usr/lib/jvm/java | |
| LOGNAME=valyo | |
| GPG_AGENT_INFO=/tmp/keyring-nLLOmx/gpg:0:1 | |
| PROFILEREAD=true | |
| XMODIFIERS=@im=local | |
| SSH_AUTH_SOCK=/tmp/keyring-nLLOmx/ssh | |
| LD_LIBRARY_PATH=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386/client:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../lib/i386:/usr/lib/R/lib:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386/client:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386: | |
| DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-BB0jCC1xVj,guid=039a60c33d8aacaf851074d10000000f | |
| SHELL=/bin/bash | |
| R_HOME=/usr/lib/R | |
| GNOME_KEYRING_PID=2049 | |
| JAVA_BINDIR=/usr/lib/jvm/java/bin | |
| MORE=-sl | |
| DESKTOP_SESSION=gnome | |
| JRE_HOME=/usr/lib/jvm/jre | |
| DISPLAY=:0.0 | |
| USER=valyo | |
| GPG_TTY=not a tty | |
| HOME=/home/valyo | |
| LESSOPEN=lessopen.sh %s | |
| CSHEDIT=emacs | |
| XSESSION_IS_UP=yes | |
| ORBIT_SOCKETDIR=/tmp/orbit-valyo | |
| FROM_HEADER= | |
| LANG=en_US.utf8 | |
| SDL_AUDIODRIVER=pulse | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.servi.internal.NodeController start | |
| INFO: [Control:Rconsole-1321280140197] Initializing R node... | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader <init> | |
| CONFIG: System URL classloader: enabled | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader <init> | |
| CONFIG: Alternative classloader: disabled | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader initRLibs | |
| CONFIG: JR library path: | |
| /home/valyo/R/i686-suse-linux-gnu-library/2.13 | |
| /usr/local/lib/R/site-library | |
| /usr/lib/R/library | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added '/home/valyo/R/i686-suse-linux-gnu-library/2.13/rJava/java' to classpath of URL loader | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader <init> | |
| CONFIG: registered JRI: /home/valyo/R/i686-suse-linux-gnu-library/2.13/rj/jri/libjri.so | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added '/home/valyo/R/i686-suse-linux-gnu-library/2.13/rj/jri/JRI.jar' to classpath of URL loader | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added '/home/valyo/R/i686-suse-linux-gnu-library/2.13/rj/server/rj.jar' to classpath of URL loader | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added '/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar' to classpath of URL loader | |
| Nov 14, 2011 3:15:40 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.REXP | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.REXP' using URL loader | |
| Nov 14, 2011 3:15:40 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.RMainLoopCallbacks | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.RMainLoopCallbacks' using URL loader | |
| Nov 14, 2011 3:15:40 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.Rengine | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.Rengine' using URL loader | |
| Nov 14, 2011 3:15:40 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.Mutex | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.Mutex' using URL loader | |
| Nov 14, 2011 3:15:40 PM RJavaClassLoader findLibrary | |
| FINER: ENTRY jri | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader findLibrary | |
| FINE: Mapping to /home/valyo/R/i686-suse-linux-gnu-library/2.13/rj/jri/libjri.so | |
| Nov 14, 2011 3:15:40 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIServer | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIServer' using URL loader | |
| Nov 14, 2011 3:15:40 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIServer$InitCallbacks | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIServer$InitCallbacks' using URL loader | |
| Nov 14, 2011 3:15:40 PM RJavaClassLoader findLibrary | |
| FINER: ENTRY jri | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader findLibrary | |
| FINE: Mapping to /home/valyo/R/i686-suse-linux-gnu-library/2.13/rj/jri/libjri.so | |
| Nov 14, 2011 3:15:40 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.RConfig | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.RConfig' using URL loader | |
| Nov 14, 2011 3:15:40 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIObjectFactory | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIObjectFactory' using URL loader | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.JRIServer initEngine | |
| FINER: Pointers: | |
| NULL = 0x81c9898 | |
| Unbound = 0x81c987c | |
| MissingArg = 0x81c9860 | |
| BaseEnv = 0x81f59fc | |
| AutoloadEnv = 0x82613ac | |
| RJTempEnv = 0x866b3d8 | |
| functionSymbol = 0x81dbea0 | |
| ifSymbol = 0x81dc0ec | |
| AssignSymbol = 0x81dbe4c | |
| xSymbol = 0x81fc3f0 | |
| zSymbol = 0x82b5900 | |
| objectSymbol = 0x82939e0 | |
| envSymbol = 0x81fb7a4 | |
| nameSymbol = 0x81c9550 | |
| realSymbol = 0x8249994 | |
| imaginarySymbol = 0x866345c | |
| newSymbol = 0x82afe78 | |
| ClassSymbol = 0x86633ec | |
| exprSymbol = 0x8200944 | |
| errorSymbol = 0x8266258 | |
| factorClassString = 0x8662de0 | |
| orderedClassString = 0x8662e00 | |
| dataframeClassString = 0x8662dc0 | |
| lengthFun = 0x81df010 | |
| complexFun = 0x866b2a4 | |
| envNameFun = 0x86645e4 | |
| headerFun = 0x86640a4 | |
| s4classFun = 0x8665cb8 | |
| slotNamesFun = 0x866f460 | |
| ReFun = 0x81e6adc | |
| ImFun = 0x81e6a88 | |
| ItemFun = 0x81dbc1c | |
| tryCatchFun = 0x82692bc | |
| evalTryCatch_errorExpr = 0x86703c8 | |
| evalTemp_classExpr = 0x86682b8 | |
| evalTemp_rmExpr = 0x8668278 | |
| evalDummyExpr = 0x8670b88 | |
| Nov 14, 2011 3:15:40 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIVectorImpl | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIVectorImpl' using URL loader | |
| Nov 14, 2011 3:15:40 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRICharacterDataImpl | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRICharacterDataImpl' using URL loader | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.server.jri.JRIServer start | |
| INFO: R engine started successfully. New Client-State: 'Connected'. | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.servi.internal.NodeServer start1 | |
| FINE: Initializing R node: Loading R package 'rj'... | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.servi.internal.NodeServer start1 | |
| FINE: Initializing R node: Preparing R workspace for first client... | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.servi.internal.NodeController start | |
| FINE: [Control:Rconsole-1321280140197] Initializing R node: R engine started and initialized. | |
| Nov 14, 2011 3:15:40 PM de.walware.rj.servi.internal.NodeController start | |
| FINE: [Control:Rconsole-1321280140197] Initializing R node: Publishing in registry... | |
| Nov 14, 2011 3:15:41 PM de.walware.rj.server.srvImpl.AbstractServerControl publishServer | |
| SEVERE: [Control:Rconsole-1321280140197] 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(UnicastServerRef.java:413) | |
| at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:267) | |
| at sun.rmi.transport.Transport$1.run(Transport.java:177) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at sun.rmi.transport.Transport.serviceCall(Transport.java:173) | |
| at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:553) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:808) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:667) | |
| at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) | |
| at java.lang.Thread.run(Thread.java:679) | |
| at sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(StreamRemoteCall.java:273) | |
| at sun.rmi.transport.StreamRemoteCall.executeCall(StreamRemoteCall.java:251) | |
| at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:377) | |
| at sun.rmi.registry.RegistryImpl_Stub.bind(Unknown Source) | |
| at java.rmi.Naming.bind(Naming.java:128) | |
| 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(UnicastServerRef.java:403) | |
| at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:267) | |
| at sun.rmi.transport.Transport$1.run(Transport.java:177) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at sun.rmi.transport.Transport.serviceCall(Transport.java:173) | |
| at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:553) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:808) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:667) | |
| at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) | |
| at java.lang.Thread.run(Thread.java:679) | |
| Caused by: java.lang.ClassNotFoundException: access to class loader denied | |
| at sun.rmi.server.LoaderHandler.loadProxyClass(LoaderHandler.java:603) | |
| at java.rmi.server.RMIClassLoader$2.loadProxyClass(RMIClassLoader.java:646) | |
| at java.rmi.server.RMIClassLoader.loadProxyClass(RMIClassLoader.java:311) | |
| at sun.rmi.server.MarshalInputStream.resolveProxyClass(MarshalInputStream.java:255) | |
| at java.io.ObjectInputStream.readProxyDesc(ObjectInputStream.java:1548) | |
| at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1510) | |
| at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1749) | |
| at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1346) | |
| at java.io.ObjectInputStream.readObject(ObjectInputStream.java:368) | |
| ... 12 more | |
| Caused by: java.security.AccessControlException: access denied (java.io.FilePermission /home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/- read) | |
| at java.security.AccessControlContext.checkPermission(AccessControlContext.java:393) | |
| at java.security.AccessController.checkPermission(AccessController.java:553) | |
| at java.lang.SecurityManager.checkPermission(SecurityManager.java:549) | |
| at sun.rmi.server.LoaderHandler$Loader.checkPermissions(LoaderHandler.java:1173) | |
| at sun.rmi.server.LoaderHandler$Loader.access$000(LoaderHandler.java:1127) | |
| at sun.rmi.server.LoaderHandler.loadProxyClass(LoaderHandler.java:569) | |
| ... 20 more | |
| Nov 14, 2011 3:15:41 PM de.walware.rj.server.srvImpl.AbstractServerControl checkCleanup | |
| INFO: [Control:Rconsole-1321280140197] 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(NativeConstructorAccessorImpl.java:57) | |
| at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) | |
| at java.lang.reflect.Constructor.newInstance(Constructor.java:532) | |
| 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(Thread.java:679) | |
| 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 2011-11-16 16:25:10.153 ----------------------------------------------- | |
| eclipse.buildId=2.5.0.201108060919 | |
| java.version=1.6.0_22 | |
| java.vendor=Sun Microsystems Inc. | |
| BootLoader constants: OS=linux, ARCH=x86, WS=gtk, NL=en_US | |
| Framework arguments: -noupdate | |
| Command-line arguments: -os linux -ws gtk -arch x86 -data @nodefault -noupdate -consolelog | |
| !ENTRY org.eclipse.core.resources 2 10035 2011-11-16 16:25:11.993 | |
| !MESSAGE The workspace exited with unsaved changes in the previous session; refreshing workspace to recover changes. | |
| !ENTRY de.walware.rj.servi 4 0 2011-11-16 16:25:17.798 | |
| !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> | |
| /usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/bin/java | |
| -classpath | |
| /home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.data_0.5.5.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.servi_0.5.3.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.client_0.5.1.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/org.eclipse.equinox.common_3.6.0.v20100503.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/org.eclipse.osgi_3.6.2.R36x_v20110210.jar | |
| -Djava.security.policy=jar:file:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar!/localhost.policy | |
| -Djava.rmi.server.codebase=file:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar | |
| -Xss16384k | |
| de.walware.rj.servi.internal.NodeController | |
| rmi://127.0.0.1:62932/Rconsole-1321457116491 | |
| -verbose | |
| </COMMAND> | |
| <STDOUT> | |
| </STDOUT> | |
| <LOG file="out.log"> | |
| (RServi) R node log | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose | |
| CONFIG: verbose mode enabled. | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose | |
| CONFIG: java properties: | |
| java.runtime.name=OpenJDK Runtime Environment | |
| sun.boot.library.path=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386 | |
| java.vm.version=20.0-b11 | |
| java.vm.vendor=Sun Microsystems Inc. | |
| java.vendor.url=http://java.sun.com/ | |
| path.separator=: | |
| java.vm.name=OpenJDK Client VM | |
| file.encoding.pkg=sun.io | |
| sun.java.launcher=SUN_STANDARD | |
| user.country=US | |
| sun.os.patch.level=unknown | |
| java.vm.specification.name=Java Virtual Machine Specification | |
| user.dir=/tmp/Rconsole-1321457116491 | |
| java.runtime.version=1.6.0_22-b22 | |
| java.awt.graphicsenv=sun.awt.X11GraphicsEnvironment | |
| java.endorsed.dirs=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/endorsed | |
| os.arch=i386 | |
| java.io.tmpdir=/tmp | |
| line.separator= | |
| java.vm.specification.vendor=Sun Microsystems Inc. | |
| os.name=Linux | |
| sun.jnu.encoding=UTF-8 | |
| java.library.path=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386/client:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../lib/i386:/usr/lib/R/lib:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386/client:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386::/usr/java/packages/lib/i386:/lib:/usr/lib | |
| java.specification.name=Java Platform API Specification | |
| java.class.version=50.0 | |
| sun.management.compiler=HotSpot Client Compiler | |
| os.version=2.6.37.6-0.7-desktop | |
| user.home=/home/valyo | |
| java.security.policy=jar:file:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar!/localhost.policy | |
| user.timezone=Europe/Stockholm | |
| java.awt.printerjob=sun.print.PSPrinterJob | |
| file.encoding=UTF-8 | |
| java.specification.version=1.6 | |
| java.class.path=/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.data_0.5.5.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.servi_0.5.3.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.client_0.5.1.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/org.eclipse.equinox.common_3.6.0.v20100503.jar:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/org.eclipse.osgi_3.6.2.R36x_v20110210.jar | |
| user.name=valyo | |
| java.vm.specification.version=1.0 | |
| sun.java.command=de.walware.rj.servi.internal.NodeController rmi://127.0.0.1:62932/Rconsole-1321457116491 -verbose | |
| java.home=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre | |
| sun.arch.data.model=32 | |
| user.language=en | |
| java.specification.vendor=Sun Microsystems Inc. | |
| java.vm.info=mixed mode | |
| java.version=1.6.0_22 | |
| java.ext.dirs=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/ext:/usr/java/packages/lib/ext | |
| sun.boot.class.path=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/resources.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/rt.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/sunrsasign.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/jsse.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/jce.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/charsets.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/netx.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/plugin.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/rhino.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/modules/jdk.boot.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/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=gnome | |
| java.rmi.server.codebase=file:/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar | |
| sun.cpu.isalist= | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose | |
| CONFIG: env variables: | |
| TERM=xterm | |
| WINDOWMANAGER=/usr/bin/gnome | |
| JAVA_HOME=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre | |
| LESSCLOSE=lessclose.sh %s %s | |
| SESSION_MANAGER=local/linux-gwrj:@/tmp/.ICE-unix/2303,unix/linux-gwrj:/tmp/.ICE-unix/2303 | |
| GNOME_DESKTOP_SESSION_ID=this-is-deprecated | |
| HOSTTYPE=i386 | |
| R_LIBS_USER=/home/valyo/R/i686-suse-linux-gnu-library/2.13 | |
| MAIL=/var/spool/mail/valyo | |
| GDMSESSION=gnome | |
| XDG_SESSION_COOKIE=7dd418d636a94d6051b870050000045b-1321456279.387065-1160989744 | |
| PWD=/home/valyo | |
| HOST=linux-gwrj | |
| HOSTNAME=linux-gwrj | |
| XCURSOR_THEME=DMZ | |
| XAUTHLOCALHOSTNAME=localhost | |
| GTK_IM_MODULE=cedilla | |
| G_FILENAME_ENCODING=@locale,UTF-8,ISO-8859-15,CP1252 | |
| G_BROKEN_FILENAMES=1 | |
| MACHTYPE=i686-suse-linux | |
| QT_SYSTEM_DIR=/usr/share/desktop-data | |
| NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat | |
| XDG_MENU_PREFIX=gnome- | |
| GDM_KEYBOARD_LAYOUT=us | |
| INPUTRC=/home/valyo/.inputrc | |
| TMPDIR=/tmp | |
| HISTSIZE=1000 | |
| XKEYSYMDB=/usr/X11R6/lib/X11/XKeysymDB | |
| PATH=/usr/lib/R/bin:/home/valyo/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games | |
| XDG_CONFIG_DIRS=/etc/xdg | |
| XNLSPATH=/usr/share/X11/nls | |
| LESS_ADVANCED_PREPROCESSOR=no | |
| LESS=-M -I -R | |
| PAGER=less | |
| PYTHONSTARTUP=/etc/pythonstart | |
| XAUTHORITY=/var/run/gdm/auth-for-valyo-MaQQl6/database | |
| GDM_LANG=en_US.utf8 | |
| SDK_HOME=/usr/lib/jvm/java | |
| WINDOWPATH=7 | |
| ALSA_CONFIG_PATH=/etc/alsa-pulse.conf | |
| USERNAME=valyo | |
| JAVA_ROOT=/usr/lib/jvm/java | |
| OSTYPE=linux | |
| LESSKEY=/etc/lesskey.bin | |
| GNOME_KEYRING_CONTROL=/tmp/keyring-g9hKuo | |
| SHLVL=0 | |
| MOZILLA_FIVE_HOME=/usr/lib/xulrunner-2.0.1 | |
| XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt | |
| MINICOM=-c on | |
| MANPATH=/usr/local/man:/usr/share/man | |
| COLORTERM=1 | |
| CPU=i686 | |
| QT_IM_SWITCHER=imsw-multi | |
| ICEAUTHORITY=/home/valyo/.ICEauthority | |
| XDG_DATA_DIRS=/usr/share | |
| NNTPSERVER=news | |
| QT_IM_MODULE=xim | |
| JDK_HOME=/usr/lib/jvm/java | |
| LOGNAME=valyo | |
| GPG_AGENT_INFO=/tmp/keyring-g9hKuo/gpg:0:1 | |
| PROFILEREAD=true | |
| XMODIFIERS=@im=local | |
| SSH_AUTH_SOCK=/tmp/keyring-g9hKuo/ssh | |
| LD_LIBRARY_PATH=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386/client:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../lib/i386:/usr/lib/R/lib:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386/client:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386: | |
| DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-LLuz4wKNVW,guid=25439aaaabb3f6d6198d277e00000010 | |
| SHELL=/bin/bash | |
| R_HOME=/usr/lib/R | |
| GNOME_KEYRING_PID=2273 | |
| JAVA_BINDIR=/usr/lib/jvm/java/bin | |
| MORE=-sl | |
| DESKTOP_SESSION=gnome | |
| JRE_HOME=/usr/lib/jvm/jre | |
| DISPLAY=:0.0 | |
| USER=valyo | |
| GPG_TTY=not a tty | |
| HOME=/home/valyo | |
| LESSOPEN=lessopen.sh %s | |
| CSHEDIT=emacs | |
| XSESSION_IS_UP=yes | |
| ORBIT_SOCKETDIR=/tmp/orbit-valyo | |
| FROM_HEADER= | |
| LANG=en_US.utf8 | |
| SDL_AUDIODRIVER=pulse | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.servi.internal.NodeController start | |
| INFO: [Control:Rconsole-1321457116491] Initializing R node... | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader <init> | |
| CONFIG: System URL classloader: enabled | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader <init> | |
| CONFIG: Alternative classloader: disabled | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader initRLibs | |
| CONFIG: JR library path: | |
| /home/valyo/R/i686-suse-linux-gnu-library/2.13 | |
| /usr/local/lib/R/site-library | |
| /usr/lib/R/library | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added '/home/valyo/R/i686-suse-linux-gnu-library/2.13/rJava/java' to classpath of URL loader | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader <init> | |
| CONFIG: registered JRI: /home/valyo/R/i686-suse-linux-gnu-library/2.13/rj/jri/libjri.so | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added '/home/valyo/R/i686-suse-linux-gnu-library/2.13/rj/jri/JRI.jar' to classpath of URL loader | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added '/home/valyo/R/i686-suse-linux-gnu-library/2.13/rj/server/rj.jar' to classpath of URL loader | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader addClassPath | |
| FINE: Added '/home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/de.walware.rj.server_0.5.5.201107191712.jar' to classpath of URL loader | |
| Nov 16, 2011 4:25:16 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.REXP | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.REXP' using URL loader | |
| Nov 16, 2011 4:25:16 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.RMainLoopCallbacks | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.RMainLoopCallbacks' using URL loader | |
| Nov 16, 2011 4:25:16 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.Rengine | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.Rengine' using URL loader | |
| Nov 16, 2011 4:25:16 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.Mutex | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.Mutex' using URL loader | |
| Nov 16, 2011 4:25:16 PM RJavaClassLoader findLibrary | |
| FINER: ENTRY jri | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader findLibrary | |
| FINE: Mapping to /home/valyo/R/i686-suse-linux-gnu-library/2.13/rj/jri/libjri.so | |
| Nov 16, 2011 4:25:16 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIServer | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIServer' using URL loader | |
| Nov 16, 2011 4:25:16 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIServer$InitCallbacks | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIServer$InitCallbacks' using URL loader | |
| Nov 16, 2011 4:25:16 PM RJavaClassLoader findLibrary | |
| FINER: ENTRY jri | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader findLibrary | |
| FINE: Mapping to /home/valyo/R/i686-suse-linux-gnu-library/2.13/rj/jri/libjri.so | |
| Nov 16, 2011 4:25:16 PM RJavaClassLoader findClass | |
| FINER: ENTRY org.rosuda.JRI.RConfig | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'org.rosuda.JRI.RConfig' using URL loader | |
| Nov 16, 2011 4:25:16 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIObjectFactory | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIObjectFactory' using URL loader | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.JRIServer initEngine | |
| FINER: Pointers: | |
| NULL = 0x81d1410 | |
| Unbound = 0x81d13f4 | |
| MissingArg = 0x81d13d8 | |
| BaseEnv = 0x81fd9fc | |
| AutoloadEnv = 0x826919c | |
| RJTempEnv = 0x86733d0 | |
| functionSymbol = 0x81e3fb8 | |
| ifSymbol = 0x81e4204 | |
| AssignSymbol = 0x81e3f64 | |
| xSymbol = 0x82043f0 | |
| zSymbol = 0x82bd810 | |
| objectSymbol = 0x829b9a8 | |
| envSymbol = 0x82037a4 | |
| nameSymbol = 0x81d10c8 | |
| realSymbol = 0x8251784 | |
| imaginarySymbol = 0x866b454 | |
| newSymbol = 0x82b7e40 | |
| ClassSymbol = 0x866b3e4 | |
| exprSymbol = 0x8208944 | |
| errorSymbol = 0x826e2f0 | |
| factorClassString = 0x866add8 | |
| orderedClassString = 0x866adf8 | |
| dataframeClassString = 0x866adb8 | |
| lengthFun = 0x81e7128 | |
| complexFun = 0x867329c | |
| envNameFun = 0x866c3bc | |
| headerFun = 0x866be7c | |
| s4classFun = 0x866d870 | |
| slotNamesFun = 0x8677008 | |
| ReFun = 0x81eeadc | |
| ImFun = 0x81eea88 | |
| ItemFun = 0x81e3d34 | |
| tryCatchFun = 0x8271354 | |
| evalTryCatch_errorExpr = 0x8678028 | |
| evalTemp_classExpr = 0x86702b0 | |
| evalTemp_rmExpr = 0x8670270 | |
| evalDummyExpr = 0x86787e8 | |
| Nov 16, 2011 4:25:16 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRIVectorImpl | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRIVectorImpl' using URL loader | |
| Nov 16, 2011 4:25:16 PM RJavaClassLoader findClass | |
| FINER: ENTRY de.walware.rj.server.jri.JRICharacterDataImpl | |
| Nov 16, 2011 4:25:16 PM de.walware.rj.server.jri.loader.JRIClassLoader findClass | |
| FINE: Found class 'de.walware.rj.server.jri.JRICharacterDataImpl' using URL loader | |
| Nov 16, 2011 4:25:17 PM de.walware.rj.server.jri.JRIServer start | |
| INFO: R engine started successfully. New Client-State: 'Connected'. | |
| Nov 16, 2011 4:25:17 PM de.walware.rj.servi.internal.NodeServer start1 | |
| FINE: Initializing R node: Loading R package 'rj'... | |
| Nov 16, 2011 4:25:17 PM de.walware.rj.servi.internal.NodeServer start1 | |
| FINE: Initializing R node: Preparing R workspace for first client... | |
| Nov 16, 2011 4:25:17 PM de.walware.rj.servi.internal.NodeController start | |
| FINE: [Control:Rconsole-1321457116491] Initializing R node: R engine started and initialized. | |
| Nov 16, 2011 4:25:17 PM de.walware.rj.servi.internal.NodeController start | |
| FINE: [Control:Rconsole-1321457116491] Initializing R node: Publishing in registry... | |
| Nov 16, 2011 4:25:17 PM de.walware.rj.server.srvImpl.AbstractServerControl publishServer | |
| SEVERE: [Control:Rconsole-1321457116491] 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(UnicastServerRef.java:413) | |
| at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:267) | |
| at sun.rmi.transport.Transport$1.run(Transport.java:177) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at sun.rmi.transport.Transport.serviceCall(Transport.java:173) | |
| at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:553) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:808) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:667) | |
| at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) | |
| at java.lang.Thread.run(Thread.java:679) | |
| at sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(StreamRemoteCall.java:273) | |
| at sun.rmi.transport.StreamRemoteCall.executeCall(StreamRemoteCall.java:251) | |
| at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:377) | |
| at sun.rmi.registry.RegistryImpl_Stub.bind(Unknown Source) | |
| at java.rmi.Naming.bind(Naming.java:128) | |
| 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(UnicastServerRef.java:403) | |
| at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:267) | |
| at sun.rmi.transport.Transport$1.run(Transport.java:177) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at sun.rmi.transport.Transport.serviceCall(Transport.java:173) | |
| at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:553) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:808) | |
| at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:667) | |
| at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) | |
| at java.lang.Thread.run(Thread.java:679) | |
| Caused by: java.lang.ClassNotFoundException: access to class loader denied | |
| at sun.rmi.server.LoaderHandler.loadProxyClass(LoaderHandler.java:603) | |
| at java.rmi.server.RMIClassLoader$2.loadProxyClass(RMIClassLoader.java:646) | |
| at java.rmi.server.RMIClassLoader.loadProxyClass(RMIClassLoader.java:311) | |
| at sun.rmi.server.MarshalInputStream.resolveProxyClass(MarshalInputStream.java:255) | |
| at java.io.ObjectInputStream.readProxyDesc(ObjectInputStream.java:1548) | |
| at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1510) | |
| at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1749) | |
| at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1346) | |
| at java.io.ObjectInputStream.readObject(ObjectInputStream.java:368) | |
| ... 12 more | |
| Caused by: java.security.AccessControlException: access denied (java.io.FilePermission /home/valyo/Desktop/Bioclipse.2.5.0.linux.gtk.x86/plugins/- read) | |
| at java.security.AccessControlContext.checkPermission(AccessControlContext.java:393) | |
| at java.security.AccessController.checkPermission(AccessController.java:553) | |
| at java.lang.SecurityManager.checkPermission(SecurityManager.java:549) | |
| at sun.rmi.server.LoaderHandler$Loader.checkPermissions(LoaderHandler.java:1173) | |
| at sun.rmi.server.LoaderHandler$Loader.access$000(LoaderHandler.java:1127) | |
| at sun.rmi.server.LoaderHandler.loadProxyClass(LoaderHandler.java:569) | |
| ... 20 more | |
| Nov 16, 2011 4:25:17 PM de.walware.rj.server.srvImpl.AbstractServerControl checkCleanup | |
| INFO: [Control:Rconsole-1321457116491] 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(NativeConstructorAccessorImpl.java:57) | |
| at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) | |
| at java.lang.reflect.Constructor.newInstance(Constructor.java:532) | |
| 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(Thread.java:679) | |
| 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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