Cytoscape does not start from terminal

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Assa Yeroslaviz

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Nov 3, 2016, 2:16:22 AM11/3/16
to cytoscape-helpdesk
Hi,
 I am trying to start Cytoscape from the terminal on a Mac (OS v. 10.11.6). This does not work. I goes to the correct folder and it starts well, giving me the message:

"Unable to find any JVMs matching version "1.7"


but continue loading, the banner Cytoscape  is shown as well as a short help description, but than a lot of errors:

Cytoscape 3.3.0

Hit '<tab>' for a list of available commands
   and '[cmd] --help' for help on a specific command.
Hit '<ctrl-d>' or 'osgi:shutdown' to shutdown Cytoscape.

Cytoscape 3.3.0> usage: cytoscape.{sh|bat} [OPTIONS]
 -h,--help             Print this message.
 -N,--network <file>   Load a network file (any format).
 -P,--props <file>     Load cytoscape properties file (Java properties
                       format) or individual property: -P name=value.
 -R,--rest <port>      Start a rest service
 -s,--session <file>   Load a cytoscape session (.cys) file.
 -S,--script <file>    Execute commands from script file
 -v,--version          Print the version number.
 -V,--vizmap <file>    Load vizmap properties file (Cytoscape VizMap
                       format).

Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Couldn't find service: org.cytoscape.util.swing.IconManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:68)
at org.cytoscape.service.util.internal.CyServiceRegistrarImpl.getService(CyServiceRegistrarImpl.java:133)
at org.cytoscape.view.vizmap.gui.internal.util.ServicesUtil.get(ServicesUtil.java:31)
at org.cytoscape.view.vizmap.gui.internal.view.VisualPropertySheetItem.updateMappingIcon(VisualPropertySheetItem.java:789)
at org.cytoscape.view.vizmap.gui.internal.view.VisualPropertySheetItem.getMappingBtn(VisualPropertySheetItem.java:603)
at org.cytoscape.view.vizmap.gui.internal.view.VisualPropertySheetItem.getTopPnl(VisualPropertySheetItem.java:433)
at org.cytoscape.view.vizmap.gui.internal.view.VisualPropertySheetItem.init(VisualPropertySheetItem.java:375)
at org.cytoscape.view.vizmap.gui.internal.view.VisualPropertySheetItem.<init>(VisualPropertySheetItem.java:144)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator.createVisualPropertySheetItems(VizMapperMediator.java:968)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator.access$2500(VizMapperMediator.java:119)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator$24.run(VizMapperMediator.java:890)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator.invokeOnEDT(VizMapperMediator.java:1433)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator.createVisualPropertySheets(VizMapperMediator.java:875)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator.updateVisualPropertySheets(VizMapperMediator.java:846)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator.access$200(VizMapperMediator.java:119)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator$22.run(VizMapperMediator.java:772)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.IllegalStateException: Invalid BundleContext.
at org.apache.felix.framework.BundleContextImpl.checkValidity(BundleContextImpl.java:514)
at org.apache.felix.framework.BundleContextImpl.getServiceReference(BundleContextImpl.java:358)
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:60)
... 29 more
Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Couldn't find service: org.cytoscape.view.vizmap.VisualMappingManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:68)
at org.cytoscape.service.util.internal.CyServiceRegistrarImpl.getService(CyServiceRegistrarImpl.java:133)
at org.cytoscape.view.vizmap.gui.internal.util.ServicesUtil.get(ServicesUtil.java:31)
at org.cytoscape.view.vizmap.gui.internal.model.VizMapperProxy.getCurrentVisualStyle(VizMapperProxy.java:139)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator$22.run(VizMapperMediator.java:770)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.IllegalStateException: Invalid BundleContext.
at org.apache.felix.framework.BundleContextImpl.checkValidity(BundleContextImpl.java:514)
at org.apache.felix.framework.BundleContextImpl.getServiceReference(BundleContextImpl.java:358)
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:60)
... 18 more
Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Couldn't find service: org.cytoscape.view.vizmap.VisualMappingManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:68)
at org.cytoscape.service.util.internal.CyServiceRegistrarImpl.getService(CyServiceRegistrarImpl.java:133)
at org.cytoscape.view.vizmap.gui.internal.util.ServicesUtil.get(ServicesUtil.java:31)
at org.cytoscape.view.vizmap.gui.internal.model.VizMapperProxy.getCurrentVisualStyle(VizMapperProxy.java:139)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator$22.run(VizMapperMediator.java:770)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.IllegalStateException: Invalid BundleContext.
at org.apache.felix.framework.BundleContextImpl.checkValidity(BundleContextImpl.java:514)
at org.apache.felix.framework.BundleContextImpl.getServiceReference(BundleContextImpl.java:358)
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:60)
... 18 more
Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Couldn't find service: org.cytoscape.view.vizmap.VisualMappingManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:68)
at org.cytoscape.service.util.internal.CyServiceRegistrarImpl.getService(CyServiceRegistrarImpl.java:133)
at org.cytoscape.view.vizmap.gui.internal.util.ServicesUtil.get(ServicesUtil.java:31)
at org.cytoscape.view.vizmap.gui.internal.model.VizMapperProxy.getCurrentVisualStyle(VizMapperProxy.java:139)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator$22.run(VizMapperMediator.java:770)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.IllegalStateException: Invalid BundleContext.
at org.apache.felix.framework.BundleContextImpl.checkValidity(BundleContextImpl.java:514)
at org.apache.felix.framework.BundleContextImpl.getServiceReference(BundleContextImpl.java:358)
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:60)
... 18 more
Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Couldn't find service: org.cytoscape.view.vizmap.VisualMappingManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:68)
at org.cytoscape.service.util.internal.CyServiceRegistrarImpl.getService(CyServiceRegistrarImpl.java:133)
at org.cytoscape.view.vizmap.gui.internal.util.ServicesUtil.get(ServicesUtil.java:31)
at org.cytoscape.view.vizmap.gui.internal.model.VizMapperProxy.getCurrentVisualStyle(VizMapperProxy.java:139)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator$22.run(VizMapperMediator.java:770)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.IllegalStateException: Invalid BundleContext.
at org.apache.felix.framework.BundleContextImpl.checkValidity(BundleContextImpl.java:514)
at org.apache.felix.framework.BundleContextImpl.getServiceReference(BundleContextImpl.java:358)
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:60)
... 18 more
Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Couldn't find service: org.cytoscape.view.vizmap.VisualMappingManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:68)
at org.cytoscape.service.util.internal.CyServiceRegistrarImpl.getService(CyServiceRegistrarImpl.java:133)
at org.cytoscape.view.vizmap.gui.internal.util.ServicesUtil.get(ServicesUtil.java:31)
at org.cytoscape.view.vizmap.gui.internal.model.VizMapperProxy.getCurrentVisualStyle(VizMapperProxy.java:139)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator$22.run(VizMapperMediator.java:770)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.IllegalStateException: Invalid BundleContext.
at org.apache.felix.framework.BundleContextImpl.checkValidity(BundleContextImpl.java:514)
at org.apache.felix.framework.BundleContextImpl.getServiceReference(BundleContextImpl.java:358)
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:60)
... 18 more
Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Couldn't find service: org.cytoscape.view.vizmap.VisualMappingManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:68)
at org.cytoscape.service.util.internal.CyServiceRegistrarImpl.getService(CyServiceRegistrarImpl.java:133)
at org.cytoscape.view.vizmap.gui.internal.util.ServicesUtil.get(ServicesUtil.java:31)
at org.cytoscape.view.vizmap.gui.internal.model.VizMapperProxy.getCurrentVisualStyle(VizMapperProxy.java:139)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator$22.run(VizMapperMediator.java:770)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.IllegalStateException: Invalid BundleContext.
at org.apache.felix.framework.BundleContextImpl.checkValidity(BundleContextImpl.java:514)
at org.apache.felix.framework.BundleContextImpl.getServiceReference(BundleContextImpl.java:358)
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:60)
... 18 more
Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Couldn't find service: org.cytoscape.view.vizmap.VisualMappingManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:68)
at org.cytoscape.service.util.internal.CyServiceRegistrarImpl.getService(CyServiceRegistrarImpl.java:133)
at org.cytoscape.view.vizmap.gui.internal.util.ServicesUtil.get(ServicesUtil.java:31)
at org.cytoscape.view.vizmap.gui.internal.model.VizMapperProxy.getCurrentVisualStyle(VizMapperProxy.java:139)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator$22.run(VizMapperMediator.java:770)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.IllegalStateException: Invalid BundleContext.
at org.apache.felix.framework.BundleContextImpl.checkValidity(BundleContextImpl.java:514)
at org.apache.felix.framework.BundleContextImpl.getServiceReference(BundleContextImpl.java:358)
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:60)
... 18 more
Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Couldn't find service: org.cytoscape.view.vizmap.VisualMappingManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:68)
at org.cytoscape.service.util.internal.CyServiceRegistrarImpl.getService(CyServiceRegistrarImpl.java:133)
at org.cytoscape.view.vizmap.gui.internal.util.ServicesUtil.get(ServicesUtil.java:31)
at org.cytoscape.view.vizmap.gui.internal.model.VizMapperProxy.getCurrentVisualStyle(VizMapperProxy.java:139)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator$22.run(VizMapperMediator.java:770)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.IllegalStateException: Invalid BundleContext.
at org.apache.felix.framework.BundleContextImpl.checkValidity(BundleContextImpl.java:514)
at org.apache.felix.framework.BundleContextImpl.getServiceReference(BundleContextImpl.java:358)
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:60)
... 18 more
Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Couldn't find service: org.cytoscape.view.vizmap.VisualMappingManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:68)
at org.cytoscape.service.util.internal.CyServiceRegistrarImpl.getService(CyServiceRegistrarImpl.java:133)
at org.cytoscape.view.vizmap.gui.internal.util.ServicesUtil.get(ServicesUtil.java:31)
at org.cytoscape.view.vizmap.gui.internal.model.VizMapperProxy.getCurrentVisualStyle(VizMapperProxy.java:139)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator$22.run(VizMapperMediator.java:770)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.IllegalStateException: Invalid BundleContext.
at org.apache.felix.framework.BundleContextImpl.checkValidity(BundleContextImpl.java:514)
at org.apache.felix.framework.BundleContextImpl.getServiceReference(BundleContextImpl.java:358)
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:60)
... 18 more
Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Couldn't find service: org.cytoscape.util.swing.IconManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:68)
at org.cytoscape.service.util.internal.CyServiceRegistrarImpl.getService(CyServiceRegistrarImpl.java:133)
at org.cytoscape.view.vizmap.gui.internal.util.ServicesUtil.get(ServicesUtil.java:31)
at org.cytoscape.view.vizmap.gui.internal.view.VisualPropertySheet.getExpandAllBtn(VisualPropertySheet.java:381)
at org.cytoscape.view.vizmap.gui.internal.view.VisualPropertySheet.getToolBarPnl(VisualPropertySheet.java:292)
at org.cytoscape.view.vizmap.gui.internal.view.VisualPropertySheet.init(VisualPropertySheet.java:274)
at org.cytoscape.view.vizmap.gui.internal.view.VisualPropertySheet.<init>(VisualPropertySheet.java:105)
at org.cytoscape.view.vizmap.gui.internal.view.VizMapperMediator$24.run(VizMapperMediator.java:885)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.IllegalStateException: Invalid BundleContext.
at org.apache.felix.framework.BundleContextImpl.checkValidity(BundleContextImpl.java:514)
at org.apache.felix.framework.BundleContextImpl.getServiceReference(BundleContextImpl.java:358)
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:60)
... 21 more

and the program quits!

whet is the problem?
I have the latest version of java 
java version "1.8.0_112"
Java(TM) SE Runtime Environment (build 1.8.0_112-b16)
Java HotSpot(TM) 64-Bit Server VM (build 25.112-b16, mixed mode)


I was able to start Cytoscape from the terminal last week. Since than I didn't change anything in Cytoscape itself. I have just updated a few files in the app ClueGO

Can someone maybe pinpoint the problem?

thanks
Assa



Bernhard

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Nov 3, 2016, 11:26:13 AM11/3/16
to cytoscape-helpdesk
Hi Assa, I am not sure if this helps, but you should probably use Cytoscape 3.4.0 and clean up the CytoscapeConfiguration folder from time to time or when you change the Cytoscape version. Make also sure that your JAVA_HOME is set to the latest jre/jdk in your case version 1.8.
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