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Created October 26, 2011 10:51
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BC2.5/Ubuntu 64bit - starting Bioclipse-R
Raw
.log
!SESSION 2011-11-14 11:46:03.647 -----------------------------------------------
eclipse.buildId=2.5.0.201108060919
java.version=1.6.0_22
java.vendor=Sun Microsystems Inc.
BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US
Framework arguments: -noupdate
Command-line arguments: -os linux -ws gtk -arch x86_64 -data @nodefault -noupdate -consolelog
!ENTRY org.eclipse.core.resources 2 10035 2011-11-14 11:46:07.402
!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 11:46:17.997
!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-6-openjdk/jre/bin/java
-classpath
/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/plugins/de.walware.rj.data_0.5.5.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/plugins/de.walware.rj.server_0.5.5.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/plugins/de.walware.rj.servi_0.5.3.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/plugins/de.walware.rj.client_0.5.1.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/plugins/org.eclipse.equinox.common_3.6.0.v20100503.jar:/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/plugins/org.eclipse.osgi_3.6.2.R36x_v20110210.jar
-Djava.security.policy=jar:file:/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/plugins/de.walware.rj.server_0.5.5.201107191712.jar!/localhost.policy
-Djava.rmi.server.codebase=file:/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/plugins/de.walware.rj.server_0.5.5.201107191712.jar
-Xss16384k
de.walware.rj.servi.internal.NodeController
rmi://127.0.0.1:59542/Rconsole-1321267577667
-verbose
</COMMAND>
<STDOUT>
</STDOUT>
<LOG file="out.log">
(RServi) R node log
Nov 14, 2011 11:46:17 AM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose
CONFIG: verbose mode enabled.
Nov 14, 2011 11:46:17 AM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose
CONFIG: java properties:
java.runtime.name=OpenJDK Runtime Environment
sun.boot.library.path=/usr/lib/jvm/java-6-openjdk/jre/lib/amd64
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 64-Bit Server 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-1321267577667
java.runtime.version=1.6.0_22-b22
java.awt.graphicsenv=sun.awt.X11GraphicsEnvironment
java.endorsed.dirs=/usr/lib/jvm/java-6-openjdk/jre/lib/endorsed
os.arch=amd64
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-6-openjdk/jre/lib/amd64/server:/usr/lib/jvm/java-6-openjdk/jre/lib/amd64:/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64:/usr/lib64/R/lib:/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server:/usr/lib/jvm/java-6-openjdk/jre/lib/amd64:/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
java.specification.name=Java Platform API Specification
java.class.version=50.0
sun.management.compiler=HotSpot 64-Bit Tiered Compilers
os.version=2.6.38-12-generic
user.home=/home/valyo
java.security.policy=jar:file:/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/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.2.5.0.2011_11_14/plugins/de.walware.rj.data_0.5.5.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/plugins/de.walware.rj.server_0.5.5.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/plugins/de.walware.rj.servi_0.5.3.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/plugins/de.walware.rj.client_0.5.1.201107191712.jar:/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/plugins/org.eclipse.equinox.common_3.6.0.v20100503.jar:/home/valyo/Desktop/Bioclipse.2.5.0.2011_11_14/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://127.0.0.1:59542/Rconsole-1321267577667 -verbose
java.home=/usr/lib/jvm/java-6-openjdk/jre
sun.arch.data.model=64
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-6-openjdk/jre/lib/ext:/usr/java/packages/lib/ext
sun.boot.class.path=/usr/lib/jvm/java-6-openjdk/jre/lib/resources.jar:/usr/lib/jvm/java-6-openjdk/jre/lib/rt.jar:/usr/lib/jvm/java-6-openjdk/jre/lib/sunrsasign.jar:/usr/lib/jvm/java-6-openjdk/jre/lib/jsse.jar:/usr/lib/jvm/java-6-openjdk/jre/lib/jce.jar:/usr/lib/jvm/java-6-openjdk/jre/lib/charsets.jar:/usr/lib/jvm/java-6-openjdk/jre/lib/netx.jar:/usr/lib/jvm/java-6-openjdk/jre/lib/plugin.jar:/usr/lib/jvm/java-6-openjdk/jre/lib/rhino.jar:/usr/lib/jvm/java-6-openjdk/jre/lib/modules/jdk.boot.jar:/usr/lib/jvm/java-6-openjdk/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.2.5.0.2011_11_14/plugins/de.walware.rj.server_0.5.5.201107191712.jar
sun.cpu.isalist=
Nov 14, 2011 11:46:17 AM de.walware.rj.server.srvImpl.AbstractServerControl initVerbose
CONFIG: env variables:
GNOME_KEYRING_CONTROL=/tmp/keyring-d1IOxi
GTK_MODULES=canberra-gtk-module
JAVA_HOME=/usr/lib/jvm/java-6-openjdk/jre
SSH_AGENT_PID=1389
SESSION_MANAGER=local/ubuntu-64:@/tmp/.ICE-unix/1337,unix/ubuntu-64:/tmp/.ICE-unix/1337
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GDMSESSION=gnome-classic
XDG_SESSION_COOKIE=20b4af3800ec6e425d835d3800000002-1321267125.151635-1374654748
XDG_DATA_DIRS=/usr/share/gnome-classic:/usr/share/gnome:/usr/local/share/:/usr/share/
MANDATORY_PATH=/usr/share/gconf/gnome-classic.mandatory.path
PWD=/home/valyo
LOGNAME=valyo
SSH_AUTH_SOCK=/tmp/keyring-d1IOxi/ssh
LD_LIBRARY_PATH=/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server:/usr/lib/jvm/java-6-openjdk/jre/lib/amd64:/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64:/usr/lib64/R/lib:/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server:/usr/lib/jvm/java-6-openjdk/jre/lib/amd64:/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-EW2OAHaGwz,guid=4da0ed150365cdd1986d19af00000009
SHELL=/bin/bash
GDM_KEYBOARD_LAYOUT=us
R_HOME=/usr/lib64/R
GNOME_KEYRING_PID=1318
LANGUAGE=en_US:en
XDG_CONFIG_DIRS=/etc/xdg/xdg-gnome-classic:/etc/xdg
PATH=/usr/lib64/R/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
DESKTOP_SESSION=gnome-classic
DISPLAY=:0.0
UBUNTU_MENUPROXY=libappmenu.so
USER=valyo
HOME=/home/valyo
XAUTHORITY=/var/run/gdm/auth-for-valyo-niO49o/database
GDM_LANG=en_US
WINDOWPATH=7
DEFAULTS_PATH=/usr/share/gconf/gnome-classic.default.path
USERNAME=valyo
ORBIT_SOCKETDIR=/tmp/orbit-valyo
LANG=en_US.UTF-8
Nov 14, 2011 11:46:17 AM de.walware.rj.servi.internal.NodeController start
INFO: [Control:Rconsole-1321267577667] Initializing R node...
Nov 14, 2011 11:46:17 AM de.walware.rj.server.jri.loader.JRIClassLoader <init>
CONFIG: System URL classloader: enabled
Nov 14, 2011 11:46:17 AM de.walware.rj.server.jri.loader.JRIClassLoader <init>
CONFIG: Alternative classloader: disabled
Nov 14, 2011 11:46:17 AM de.walware.rj.server.jri.loader.JRIClassLoader initRLibs
CONFIG: JR library path:
/usr/local/lib64/R/site-library
/usr/lib64/R/library
Nov 14, 2011 11:46:17 AM de.walware.rj.server.jri.loader.JRIClassLoader <init>
SEVERE: Path to rj package not found. Use R_LIBS or java property 'de.walware.rj.rpkg.path' to specify the location.
Nov 14, 2011 11:46:17 AM de.walware.rj.server.srvImpl.AbstractServerControl initREngine
SEVERE: [Control:Rconsole-1321267577667] init JRI/Rengine failed.
java.lang.RuntimeException: Path to rj package not found. Use R_LIBS or java property 'de.walware.rj.rpkg.path' to specify the location.
at de.walware.rj.server.jri.loader.JRIClassLoader.<init>(JRIClassLoader.java:276)
at RJavaClassLoader.<init>(RJavaClassLoader.java:47)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
at java.lang.Class.newInstance0(Class.java:372)
at java.lang.Class.newInstance(Class.java:325)
at de.walware.rj.server.jri.loader.JRIClassLoader.getRJavaClassLoader(JRIClassLoader.java:44)
at de.walware.rj.server.jri.loader.JRIServerLoader.loadServer(JRIServerLoader.java:47)
at de.walware.rj.server.srvImpl.AbstractServerControl.initREngine(AbstractServerControl.java:145)
at de.walware.rj.servi.internal.NodeController.start(NodeController.java:60)
at de.walware.rj.servi.internal.NodeController.main(NodeController.java:48)
</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 = 145).
at de.walware.rj.servi.internal.LocalNodeFactory.createNode(LocalNodeFactory.java:393)
... 49 more
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