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Gephi on OS X Mavericks?

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Gephi on OS X Mavericks?

Postby francis_flavin » 23 Oct 2013 06:49

So, has anybody run Gephi 0.8.2 on OS X Mavericks yet? If so, how well did Gephi run? Thanks!

Francis
francis_flavin
 
Posts: 64
Joined: 21 Jan 2012 19:34
Location: Washington, DC, USA

Re: Gephi on OS X Mavericks?

Postby hawaiikaos » 23 Oct 2013 20:10

I just tried running it and it immediately crashes. I get this error code in the console:

23/10/2013 19:09:50.097 com.apple.launchd.peruser.501[415]: (org.gephi.22208[5492]) Exited with code: 2

EDIT:

Just upgraded something* with Java and now it opens.

(*sorry not an expert with this. OSX threw up a dialog box asking to install something updated with Java)
Last edited by hawaiikaos on 23 Oct 2013 21:01, edited 1 time in total.
hawaiikaos
 
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Joined: 23 Oct 2013 20:08
Location: United Kingdom

Re: Gephi on OS X Mavericks?

Postby bryanleroylewis » 23 Oct 2013 20:19

I installed the OSX 10.9 Java package from apple and i get Gephi to load but its not opening previously saved .gephi files nor plain .gexf files (that had been previously loading). Seems to parse the file fine as the "Content" is populated with nodes / edges properly, but no graphics load.

Icon in bottom right shows:
Unexpected Error "NoClassDefFound: apple/awt/ComponentModule
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Posts: 1
Joined: 23 Oct 2013 20:12

Re: Gephi on OS X Mavericks?

Postby svuille » 24 Oct 2013 14:13

A true nightmare here. I freshly upgraded to OS X 10.9 (Mavericks), which calls for a fresh install of JAVA. Installed both the latest JAVA JDK and JRE (7u45). Gephi 0.82 hangs on the infamous "unable to load libjogl_awt.jnilib", Gephi 0.81 refuse to start (console indicates error 2, as mentioned in previous post). I have tried everything (uninstall and reinstall Gephi, JDK, JRE, in various order, delete gephi Application Support files)

This is really bad as I need Gephi for my university class. Any help would be much appreciated.
svuille
 
Posts: 1
Joined: 24 Oct 2013 14:08

Re: Gephi on OS X Mavericks?

Postby francis_flavin » 24 Oct 2013 16:12

Sorry, all to hear of the difficulties you're having. Hawaiikaos, are you able to read your old .gephi files in Mavericks, or are you having a problem like bryanleroylewis is having? Thanks, all for updates.
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Posts: 64
Joined: 21 Jan 2012 19:34
Location: Washington, DC, USA

Re: Gephi on OS X Mavericks?

Postby graphjunkie » 24 Oct 2013 22:46

Registered to report the same problem, macbook pro, upgraded to maverick, there was some libjogl error so I reinstalled java 6, it loads gephi fine, however;
1) graph doesn't work, hovering mouse displays "blue beach ball" mouse cursor.
2) Clicking on data laboratory - buttons freezes in depressed state, entire gui freezes, including menubar up to, however OSX does NOT report it as "Not responding"

the entire gui is unresponsive

Terminal does not report error
$ /Applications/Gephi.app/Contents/Resources/gephi/bin/gephi
Loading native libraries
Current Version is 082
# Nodes loaded: 188875
# Edges loaded: 628837

there is no gephi string in Console log either.

sent control + \ signal
caused this to happen
Code: Select all
^\2013-10-24 22:41:59
Full thread dump Java HotSpot(TM) 64-Bit Server VM (23.25-b01 mixed mode):

"sampler-awt" daemon prio=5 tid=0x00007fa2b2c20000 nid=0xa617 in Object.wait() [0x0000000111b85000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000064c06f530> (a java.util.TaskQueue)
   at java.util.TimerThread.mainLoop(Timer.java:552)
   - locked <0x000000064c06f530> (a java.util.TaskQueue)
   at java.util.TimerThread.run(Timer.java:505)

"DHNS View Destructor" daemon prio=5 tid=0x00007fa2b1a79800 nid=0xeb07 in Object.wait() [0x0000000119f03000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x0000000638b64278> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.graph.dhns.core.GraphStructure$ViewDestructorThread.run(GraphStructure.java:240)
   - locked <0x0000000638b64278> (a java.lang.Object)

"attribute-event-bus" daemon prio=5 tid=0x00007fa2b192e800 nid=0xea07 in Object.wait() [0x0000000119e00000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00000006399eaab8> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.data.attributes.event.AttributeEventManager.run(AttributeEventManager.java:137)
   - locked <0x00000006399eaab8> (a java.lang.Object)
   at java.lang.Thread.run(Thread.java:724)

"graph-event-bus" daemon prio=5 tid=0x00007fa2b1742800 nid=0xf81b in Object.wait() [0x0000000119cfd000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00000006399eaba0> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.graph.dhns.core.EventManager.run(EventManager.java:134)
   - locked <0x00000006399eaba0> (a java.lang.Object)
   at java.lang.Thread.run(Thread.java:724)

"Timer-0" daemon prio=5 tid=0x00007fa2ab157800 nid=0xe603 in Object.wait() [0x0000000115e84000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d9515a8> (a java.util.TaskQueue)
   at java.lang.Object.wait(Object.java:503)
   at java.util.TimerThread.mainLoop(Timer.java:526)
   - locked <0x000000061d9515a8> (a java.util.TaskQueue)
   at java.util.TimerThread.run(Timer.java:505)

"Dynamic Set Visible Interval Thread" daemon prio=5 tid=0x00007fa2ab001000 nid=0xe503 in Object.wait() [0x0000000115666000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d98fe48> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.dynamic.DynamicControllerImpl$SetVisibleIntervalThread.run(DynamicControllerImpl.java:254)
   - locked <0x000000061d98fe48> (a java.lang.Object)

"Dynamic Model EventDispatchThread" daemon prio=5 tid=0x00007fa2b18cc800 nid=0xa907 in Object.wait() [0x0000000115563000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d98fed0> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.dynamic.DynamicControllerImpl$DynamicModelEventDispatchThread.run(DynamicControllerImpl.java:299)
   - locked <0x000000061d98fed0> (a java.lang.Object)

"DestroyJavaVM" prio=5 tid=0x00007fa2ad859800 nid=0x1703 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"TimerQueue" daemon prio=5 tid=0x00007fa2acbed800 nid=0xdd2f waiting on condition [0x0000000112c40000]
   java.lang.Thread.State: WAITING (parking)
   at sun.misc.Unsafe.park(Native Method)
   - parking to wait for  <0x000000061d764600> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
   at java.util.concurrent.locks.LockSupport.park(LockSupport.java:186)
   at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2043)
   at java.util.concurrent.DelayQueue.take(DelayQueue.java:209)
   at javax.swing.TimerQueue.run(TimerQueue.java:171)
   at java.lang.Thread.run(Thread.java:724)

"Thread-3" daemon prio=5 tid=0x00007fa2acc53800 nid=0xde2f in Object.wait() [0x0000000115460000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d7646c8> (a java.util.LinkedList)
   at java.lang.Object.wait(Object.java:503)
   at java.util.prefs.AbstractPreferences$EventDispatchThread.run(AbstractPreferences.java:1476)
   - locked <0x000000061d7646c8> (a java.util.LinkedList)

"File Watcher" daemon prio=5 tid=0x00007fa2abb69800 nid=0xdc03 waiting on condition [0x0000000112485000]
   java.lang.Thread.State: WAITING (parking)
   at sun.misc.Unsafe.park(Native Method)
   - parking to wait for  <0x000000061d764790> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
   at java.util.concurrent.locks.LockSupport.park(LockSupport.java:186)
   at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2043)
   at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)
   at org.netbeans.modules.masterfs.watcher.macosx.OSXNotifier.nextEvent(OSXNotifier.java:105)
   at org.netbeans.modules.masterfs.providers.Notifier$1.nextEvent(Notifier.java:119)
   at org.netbeans.modules.masterfs.watcher.Watcher$Ext.run(Watcher.java:301)
   at java.lang.Thread.run(Thread.java:724)

"Thread-2" daemon prio=5 tid=0x00007fa2abc66800 nid=0xd52f runnable [0x0000000112256000]
   java.lang.Thread.State: RUNNABLE
   at com.sun.jna.Native.invokeVoid(Native Method)
   at com.sun.jna.Function.invoke(Function.java:328)
   at com.sun.jna.Function.invoke(Function.java:276)
   at com.sun.jna.Library$Handler.invoke(Library.java:216)
   at com.sun.proxy.$Proxy3.CFRunLoopRun(Unknown Source)
   at org.netbeans.modules.masterfs.watcher.macosx.OSXNotifier$1.run(OSXNotifier.java:126)
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
   at java.lang.Thread.run(Thread.java:724)

"AWT-EventQueue-0" prio=5 tid=0x00007fa2aba0c000 nid=0xb803 in Object.wait() [0x000000010e21b000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061da48fc0> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at com.sun.opengl.impl.GLContextLock.lock(GLContextLock.java:73)
   - locked <0x000000061da48fc0> (a java.lang.Object)
   at com.sun.opengl.impl.GLContextImpl.destroy(GLContextImpl.java:203)
   at javax.media.opengl.GLCanvas$DestroyAction.run(GLCanvas.java:471)
   at javax.media.opengl.GLCanvas.removeNotify(GLCanvas.java:320)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at org.netbeans.swing.tabcontrol.TabbedContainer.removeNotify(TabbedContainer.java:960)
   at org.netbeans.core.windows.view.ui.tabcontrol.TabbedAdapter.removeNotify(TabbedAdapter.java:331)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.remove(Container.java:1199)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at java.awt.Container.remove(Container.java:1257)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at org.netbeans.core.windows.view.ui.DesktopImpl.setViewComponent(DesktopImpl.java:166)
   at org.netbeans.core.windows.view.ui.DesktopImpl.setSplitRoot(DesktopImpl.java:144)
   at org.netbeans.core.windows.view.ViewHierarchy.setSplitRootIntoDesktop(ViewHierarchy.java:659)
   at org.netbeans.core.windows.view.ViewHierarchy.updateDesktop(ViewHierarchy.java:700)
   at org.netbeans.core.windows.view.DefaultView.changeGUI(DefaultView.java:262)
   at org.netbeans.core.windows.ViewRequestor.dispatchRequest(ViewRequestor.java:273)
   at org.netbeans.core.windows.ViewRequestor.processRequest(ViewRequestor.java:249)
   at org.netbeans.core.windows.ViewRequestor.postRequest(ViewRequestor.java:187)
   at org.netbeans.core.windows.ViewRequestor.scheduleRequest(ViewRequestor.java:127)
   at org.netbeans.core.windows.Central.setEditorAreaConstraints(Central.java:281)
   at org.netbeans.core.windows.WindowManagerImpl.setEditorAreaConstraints(WindowManagerImpl.java:787)
   at org.netbeans.core.windows.PersistenceHandler.load(PersistenceHandler.java:182)
   at org.netbeans.core.windows.WindowSystemImpl.load(WindowSystemImpl.java:81)
   at org.netbeans.core.windows.WindowManagerImpl.switchRole(WindowManagerImpl.java:1884)
   at org.netbeans.core.windows.WindowManagerImpl.setRole(WindowManagerImpl.java:1838)
   at org.netbeans.core.windows.WindowManagerImpl.setRole(WindowManagerImpl.java:1823)
   at org.gephi.perspective.PerspectiveControllerImpl.openAndCloseMembers(PerspectiveControllerImpl.java:164)
   at org.gephi.perspective.PerspectiveControllerImpl.selectPerspective(PerspectiveControllerImpl.java:157)
   at org.gephi.desktop.perspective.BannerComponent$2.actionPerformed(BannerComponent.java:106)
   at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
   at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
   at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
   at javax.swing.JToggleButton$ToggleButtonModel.setPressed(JToggleButton.java:308)
   at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
   at java.awt.Component.processMouseEvent(Component.java:6505)
   at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
   at java.awt.Component.processEvent(Component.java:6270)
   at java.awt.Container.processEvent(Container.java:2229)
   at java.awt.Component.dispatchEventImpl(Component.java:4861)
   at java.awt.Container.dispatchEventImpl(Container.java:2287)
   at java.awt.Component.dispatchEvent(Component.java:4687)
   at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
   at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
   at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
   at java.awt.Container.dispatchEventImpl(Container.java:2273)
   at java.awt.Window.dispatchEventImpl(Window.java:2719)
   at java.awt.Component.dispatchEvent(Component.java:4687)
   at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
   at java.awt.EventQueue.access$200(EventQueue.java:103)
   at java.awt.EventQueue$3.run(EventQueue.java:694)
   at java.awt.EventQueue$3.run(EventQueue.java:692)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
   at java.awt.EventQueue$4.run(EventQueue.java:708)
   at java.awt.EventQueue$4.run(EventQueue.java:706)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
   at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
   at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:158)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
   at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
   at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
   at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

"Java2D Disposer" daemon prio=5 tid=0x00007fa2ab9bc000 nid=0xb703 in Object.wait() [0x000000010e0b1000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6130> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
   - locked <0x000000061d0e6130> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:151)
   at sun.java2d.Disposer.run(Disposer.java:145)
   at java.lang.Thread.run(Thread.java:724)

"Java2D Queue Flusher" daemon prio=5 tid=0x00007fa2ae811800 nid=0xad07 in Object.wait() [0x000000010ce4f000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6170> (a sun.java2d.opengl.OGLRenderQueue$QueueFlusher)
   at sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run(OGLRenderQueue.java:208)
   - locked <0x000000061d0e6170> (a sun.java2d.opengl.OGLRenderQueue$QueueFlusher)

"RequestProcessor queue manager" daemon prio=5 tid=0x00007fa2aa985000 nid=0xa707 in Object.wait() [0x000000010cd4c000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6258> (a java.lang.Class for org.openide.util.RequestProcessor$TickTac)
   at org.openide.util.RequestProcessor$TickTac.obtainFirst(RequestProcessor.java:2249)
   - locked <0x000000061d0e6258> (a java.lang.Class for org.openide.util.RequestProcessor$TickTac)
   at org.openide.util.RequestProcessor$TickTac.run(RequestProcessor.java:2225)

"AWT-Shutdown" prio=5 tid=0x00007fa2ae802800 nid=0x4407 in Object.wait() [0x00000001087cd000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6628> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:287)
   - locked <0x000000061d0e6628> (a java.lang.Object)
   at java.lang.Thread.run(Thread.java:724)

"AppKit Thread" daemon prio=5 tid=0x00007fa2ab0d8000 nid=0x507 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"CLI Requests Server" daemon prio=5 tid=0x00007fa2ab95e000 nid=0x3f03 runnable [0x000000010847c000]
   java.lang.Thread.State: RUNNABLE
   at java.net.PlainSocketImpl.socketAccept(Native Method)
   at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:398)
   at java.net.ServerSocket.implAccept(ServerSocket.java:530)
   at java.net.ServerSocket.accept(ServerSocket.java:498)
   at org.netbeans.CLIHandler$Server.run(CLIHandler.java:1085)

"Active Reference Queue Daemon" daemon prio=5 tid=0x00007fa2ac84d800 nid=0x3e03 in Object.wait() [0x0000000108379000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e68e8> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
   - locked <0x000000061d0e68e8> (a java.lang.ref.ReferenceQueue$Lock)
   at org.openide.util.lookup.implspi.ActiveQueue$Daemon.run(ActiveQueue.java:180)
   - locked <0x000000061d0e68e8> (a java.lang.ref.ReferenceQueue$Lock)

"Service Thread" daemon prio=5 tid=0x00007fa2ab83d800 nid=0x3c03 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread1" daemon prio=5 tid=0x00007fa2ab83c800 nid=0x3b03 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" daemon prio=5 tid=0x00007fa2ab83c000 nid=0x3a03 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" daemon prio=5 tid=0x00007fa2ab83b000 nid=0x3903 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=5 tid=0x00007fa2ab803000 nid=0x2603 in Object.wait() [0x000000010799e000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6bd0> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
   - locked <0x000000061d0e6bd0> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:151)
   at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:189)

"Reference Handler" daemon prio=5 tid=0x00007fa2ab802000 nid=0x2503 in Object.wait() [0x000000010789b000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e62f0> (a java.lang.ref.Reference$Lock)
   at java.lang.Object.wait(Object.java:503)
   at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:133)
   - locked <0x000000061d0e62f0> (a java.lang.ref.Reference$Lock)

"VM Thread" prio=5 tid=0x00007fa2ab051000 nid=0x2403 runnable

"VM Periodic Task Thread" prio=5 tid=0x00007fa2aa80a800 nid=0x3d03 waiting on condition

JNI global references: 1423

Heap
 def new generation   total 592128K, used 496078K [0x000000052e200000, 0x0000000556480000, 0x000000061d0a0000)
  eden space 526336K,  94% used [0x000000052e200000, 0x000000054c673818, 0x000000054e400000)
  from space 65792K,   0% used [0x000000054e400000, 0x000000054e400000, 0x0000000552440000)
  to   space 65792K,   0% used [0x0000000552440000, 0x0000000552440000, 0x0000000556480000)
 tenured generation   total 1315748K, used 789446K [0x000000061d0a0000, 0x000000066d589000, 0x00000007fae00000)
   the space 1315748K,  59% used [0x000000061d0a0000, 0x000000064d391aa8, 0x000000064d391c00, 0x000000066d589000)
 compacting perm gen  total 46720K, used 46682K [0x00000007fae00000, 0x00000007fdba0000, 0x0000000800000000)
   the space 46720K,  99% used [0x00000007fae00000, 0x00000007fdb96908, 0x00000007fdb96a00, 0x00000007fdba0000)
No shared spaces configured.

^\2013-10-24 22:42:21
Full thread dump Java HotSpot(TM) 64-Bit Server VM (23.25-b01 mixed mode):

"sampler-awt" daemon prio=5 tid=0x00007fa2b2c20000 nid=0xa617 in Object.wait() [0x0000000111b85000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000064c06f530> (a java.util.TaskQueue)
   at java.util.TimerThread.mainLoop(Timer.java:552)
   - locked <0x000000064c06f530> (a java.util.TaskQueue)
   at java.util.TimerThread.run(Timer.java:505)

"DHNS View Destructor" daemon prio=5 tid=0x00007fa2b1a79800 nid=0xeb07 in Object.wait() [0x0000000119f03000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x0000000638b64278> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.graph.dhns.core.GraphStructure$ViewDestructorThread.run(GraphStructure.java:240)
   - locked <0x0000000638b64278> (a java.lang.Object)

"attribute-event-bus" daemon prio=5 tid=0x00007fa2b192e800 nid=0xea07 in Object.wait() [0x0000000119e00000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00000006399eaab8> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.data.attributes.event.AttributeEventManager.run(AttributeEventManager.java:137)
   - locked <0x00000006399eaab8> (a java.lang.Object)
   at java.lang.Thread.run(Thread.java:724)

"graph-event-bus" daemon prio=5 tid=0x00007fa2b1742800 nid=0xf81b in Object.wait() [0x0000000119cfd000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00000006399eaba0> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.graph.dhns.core.EventManager.run(EventManager.java:134)
   - locked <0x00000006399eaba0> (a java.lang.Object)
   at java.lang.Thread.run(Thread.java:724)

"Timer-0" daemon prio=5 tid=0x00007fa2ab157800 nid=0xe603 in Object.wait() [0x0000000115e84000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d9515a8> (a java.util.TaskQueue)
   at java.lang.Object.wait(Object.java:503)
   at java.util.TimerThread.mainLoop(Timer.java:526)
   - locked <0x000000061d9515a8> (a java.util.TaskQueue)
   at java.util.TimerThread.run(Timer.java:505)

"Dynamic Set Visible Interval Thread" daemon prio=5 tid=0x00007fa2ab001000 nid=0xe503 in Object.wait() [0x0000000115666000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d98fe48> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.dynamic.DynamicControllerImpl$SetVisibleIntervalThread.run(DynamicControllerImpl.java:254)
   - locked <0x000000061d98fe48> (a java.lang.Object)

"Dynamic Model EventDispatchThread" daemon prio=5 tid=0x00007fa2b18cc800 nid=0xa907 in Object.wait() [0x0000000115563000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d98fed0> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.dynamic.DynamicControllerImpl$DynamicModelEventDispatchThread.run(DynamicControllerImpl.java:299)
   - locked <0x000000061d98fed0> (a java.lang.Object)

"DestroyJavaVM" prio=5 tid=0x00007fa2ad859800 nid=0x1703 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"TimerQueue" daemon prio=5 tid=0x00007fa2acbed800 nid=0xdd2f waiting on condition [0x0000000112c40000]
   java.lang.Thread.State: WAITING (parking)
   at sun.misc.Unsafe.park(Native Method)
   - parking to wait for  <0x000000061d764600> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
   at java.util.concurrent.locks.LockSupport.park(LockSupport.java:186)
   at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2043)
   at java.util.concurrent.DelayQueue.take(DelayQueue.java:209)
   at javax.swing.TimerQueue.run(TimerQueue.java:171)
   at java.lang.Thread.run(Thread.java:724)

"Thread-3" daemon prio=5 tid=0x00007fa2acc53800 nid=0xde2f in Object.wait() [0x0000000115460000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d7646c8> (a java.util.LinkedList)
   at java.lang.Object.wait(Object.java:503)
   at java.util.prefs.AbstractPreferences$EventDispatchThread.run(AbstractPreferences.java:1476)
   - locked <0x000000061d7646c8> (a java.util.LinkedList)

"File Watcher" daemon prio=5 tid=0x00007fa2abb69800 nid=0xdc03 waiting on condition [0x0000000112485000]
   java.lang.Thread.State: WAITING (parking)
   at sun.misc.Unsafe.park(Native Method)
   - parking to wait for  <0x000000061d764790> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
   at java.util.concurrent.locks.LockSupport.park(LockSupport.java:186)
   at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2043)
   at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)
   at org.netbeans.modules.masterfs.watcher.macosx.OSXNotifier.nextEvent(OSXNotifier.java:105)
   at org.netbeans.modules.masterfs.providers.Notifier$1.nextEvent(Notifier.java:119)
   at org.netbeans.modules.masterfs.watcher.Watcher$Ext.run(Watcher.java:301)
   at java.lang.Thread.run(Thread.java:724)

"Thread-2" daemon prio=5 tid=0x00007fa2abc66800 nid=0xd52f runnable [0x0000000112256000]
   java.lang.Thread.State: RUNNABLE
   at com.sun.jna.Native.invokeVoid(Native Method)
   at com.sun.jna.Function.invoke(Function.java:328)
   at com.sun.jna.Function.invoke(Function.java:276)
   at com.sun.jna.Library$Handler.invoke(Library.java:216)
   at com.sun.proxy.$Proxy3.CFRunLoopRun(Unknown Source)
   at org.netbeans.modules.masterfs.watcher.macosx.OSXNotifier$1.run(OSXNotifier.java:126)
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
   at java.lang.Thread.run(Thread.java:724)

"AWT-EventQueue-0" prio=5 tid=0x00007fa2aba0c000 nid=0xb803 in Object.wait() [0x000000010e21b000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061da48fc0> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at com.sun.opengl.impl.GLContextLock.lock(GLContextLock.java:73)
   - locked <0x000000061da48fc0> (a java.lang.Object)
   at com.sun.opengl.impl.GLContextImpl.destroy(GLContextImpl.java:203)
   at javax.media.opengl.GLCanvas$DestroyAction.run(GLCanvas.java:471)
   at javax.media.opengl.GLCanvas.removeNotify(GLCanvas.java:320)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at org.netbeans.swing.tabcontrol.TabbedContainer.removeNotify(TabbedContainer.java:960)
   at org.netbeans.core.windows.view.ui.tabcontrol.TabbedAdapter.removeNotify(TabbedAdapter.java:331)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.remove(Container.java:1199)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at java.awt.Container.remove(Container.java:1257)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at org.netbeans.core.windows.view.ui.DesktopImpl.setViewComponent(DesktopImpl.java:166)
   at org.netbeans.core.windows.view.ui.DesktopImpl.setSplitRoot(DesktopImpl.java:144)
   at org.netbeans.core.windows.view.ViewHierarchy.setSplitRootIntoDesktop(ViewHierarchy.java:659)
   at org.netbeans.core.windows.view.ViewHierarchy.updateDesktop(ViewHierarchy.java:700)
   at org.netbeans.core.windows.view.DefaultView.changeGUI(DefaultView.java:262)
   at org.netbeans.core.windows.ViewRequestor.dispatchRequest(ViewRequestor.java:273)
   at org.netbeans.core.windows.ViewRequestor.processRequest(ViewRequestor.java:249)
   at org.netbeans.core.windows.ViewRequestor.postRequest(ViewRequestor.java:187)
   at org.netbeans.core.windows.ViewRequestor.scheduleRequest(ViewRequestor.java:127)
   at org.netbeans.core.windows.Central.setEditorAreaConstraints(Central.java:281)
   at org.netbeans.core.windows.WindowManagerImpl.setEditorAreaConstraints(WindowManagerImpl.java:787)
   at org.netbeans.core.windows.PersistenceHandler.load(PersistenceHandler.java:182)
   at org.netbeans.core.windows.WindowSystemImpl.load(WindowSystemImpl.java:81)
   at org.netbeans.core.windows.WindowManagerImpl.switchRole(WindowManagerImpl.java:1884)
   at org.netbeans.core.windows.WindowManagerImpl.setRole(WindowManagerImpl.java:1838)
   at org.netbeans.core.windows.WindowManagerImpl.setRole(WindowManagerImpl.java:1823)
   at org.gephi.perspective.PerspectiveControllerImpl.openAndCloseMembers(PerspectiveControllerImpl.java:164)
   at org.gephi.perspective.PerspectiveControllerImpl.selectPerspective(PerspectiveControllerImpl.java:157)
   at org.gephi.desktop.perspective.BannerComponent$2.actionPerformed(BannerComponent.java:106)
   at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
   at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
   at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
   at javax.swing.JToggleButton$ToggleButtonModel.setPressed(JToggleButton.java:308)
   at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
   at java.awt.Component.processMouseEvent(Component.java:6505)
   at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
   at java.awt.Component.processEvent(Component.java:6270)
   at java.awt.Container.processEvent(Container.java:2229)
   at java.awt.Component.dispatchEventImpl(Component.java:4861)
   at java.awt.Container.dispatchEventImpl(Container.java:2287)
   at java.awt.Component.dispatchEvent(Component.java:4687)
   at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
   at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
   at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
   at java.awt.Container.dispatchEventImpl(Container.java:2273)
   at java.awt.Window.dispatchEventImpl(Window.java:2719)
   at java.awt.Component.dispatchEvent(Component.java:4687)
   at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
   at java.awt.EventQueue.access$200(EventQueue.java:103)
   at java.awt.EventQueue$3.run(EventQueue.java:694)
   at java.awt.EventQueue$3.run(EventQueue.java:692)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
   at java.awt.EventQueue$4.run(EventQueue.java:708)
   at java.awt.EventQueue$4.run(EventQueue.java:706)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
   at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
   at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:158)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
   at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
   at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
   at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

"Java2D Disposer" daemon prio=5 tid=0x00007fa2ab9bc000 nid=0xb703 in Object.wait() [0x000000010e0b1000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6130> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
   - locked <0x000000061d0e6130> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:151)
   at sun.java2d.Disposer.run(Disposer.java:145)
   at java.lang.Thread.run(Thread.java:724)

"Java2D Queue Flusher" daemon prio=5 tid=0x00007fa2ae811800 nid=0xad07 in Object.wait() [0x000000010ce4f000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6170> (a sun.java2d.opengl.OGLRenderQueue$QueueFlusher)
   at sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run(OGLRenderQueue.java:208)
   - locked <0x000000061d0e6170> (a sun.java2d.opengl.OGLRenderQueue$QueueFlusher)

"RequestProcessor queue manager" daemon prio=5 tid=0x00007fa2aa985000 nid=0xa707 in Object.wait() [0x000000010cd4c000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6258> (a java.lang.Class for org.openide.util.RequestProcessor$TickTac)
   at org.openide.util.RequestProcessor$TickTac.obtainFirst(RequestProcessor.java:2249)
   - locked <0x000000061d0e6258> (a java.lang.Class for org.openide.util.RequestProcessor$TickTac)
   at org.openide.util.RequestProcessor$TickTac.run(RequestProcessor.java:2225)

"AWT-Shutdown" prio=5 tid=0x00007fa2ae802800 nid=0x4407 in Object.wait() [0x00000001087cd000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6628> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:287)
   - locked <0x000000061d0e6628> (a java.lang.Object)
   at java.lang.Thread.run(Thread.java:724)

"AppKit Thread" daemon prio=5 tid=0x00007fa2ab0d8000 nid=0x507 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"CLI Requests Server" daemon prio=5 tid=0x00007fa2ab95e000 nid=0x3f03 runnable [0x000000010847c000]
   java.lang.Thread.State: RUNNABLE
   at java.net.PlainSocketImpl.socketAccept(Native Method)
   at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:398)
   at java.net.ServerSocket.implAccept(ServerSocket.java:530)
   at java.net.ServerSocket.accept(ServerSocket.java:498)
   at org.netbeans.CLIHandler$Server.run(CLIHandler.java:1085)

"Active Reference Queue Daemon" daemon prio=5 tid=0x00007fa2ac84d800 nid=0x3e03 in Object.wait() [0x0000000108379000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e68e8> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
   - locked <0x000000061d0e68e8> (a java.lang.ref.ReferenceQueue$Lock)
   at org.openide.util.lookup.implspi.ActiveQueue$Daemon.run(ActiveQueue.java:180)
   - locked <0x000000061d0e68e8> (a java.lang.ref.ReferenceQueue$Lock)

"Service Thread" daemon prio=5 tid=0x00007fa2ab83d800 nid=0x3c03 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread1" daemon prio=5 tid=0x00007fa2ab83c800 nid=0x3b03 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" daemon prio=5 tid=0x00007fa2ab83c000 nid=0x3a03 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" daemon prio=5 tid=0x00007fa2ab83b000 nid=0x3903 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=5 tid=0x00007fa2ab803000 nid=0x2603 in Object.wait() [0x000000010799e000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6bd0> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
   - locked <0x000000061d0e6bd0> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:151)
   at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:189)

"Reference Handler" daemon prio=5 tid=0x00007fa2ab802000 nid=0x2503 in Object.wait() [0x000000010789b000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e62f0> (a java.lang.ref.Reference$Lock)
   at java.lang.Object.wait(Object.java:503)
   at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:133)
   - locked <0x000000061d0e62f0> (a java.lang.ref.Reference$Lock)

"VM Thread" prio=5 tid=0x00007fa2ab051000 nid=0x2403 runnable

"VM Periodic Task Thread" prio=5 tid=0x00007fa2aa80a800 nid=0x3d03 waiting on condition

JNI global references: 1423

Heap
 def new generation   total 592128K, used 21137K [0x000000052e200000, 0x0000000556480000, 0x000000061d0a0000)
  eden space 526336K,   2% used [0x000000052e200000, 0x000000052ef57648, 0x000000054e400000)
  from space 65792K,  11% used [0x0000000552440000, 0x0000000552b8d0b0, 0x0000000556480000)
  to   space 65792K,   0% used [0x000000054e400000, 0x000000054e400000, 0x0000000552440000)
 tenured generation   total 1315748K, used 789446K [0x000000061d0a0000, 0x000000066d589000, 0x00000007fae00000)
   the space 1315748K,  59% used [0x000000061d0a0000, 0x000000064d391aa8, 0x000000064d391c00, 0x000000066d589000)
 compacting perm gen  total 46720K, used 46682K [0x00000007fae00000, 0x00000007fdba0000, 0x0000000800000000)
   the space 46720K,  99% used [0x00000007fae00000, 0x00000007fdb96908, 0x00000007fdb96a00, 0x00000007fdba0000)
No shared spaces configured.

^\2013-10-24 22:42:21
Full thread dump Java HotSpot(TM) 64-Bit Server VM (23.25-b01 mixed mode):

"sampler-awt" daemon prio=5 tid=0x00007fa2b2c20000 nid=0xa617 in Object.wait() [0x0000000111b85000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000064c06f530> (a java.util.TaskQueue)
   at java.util.TimerThread.mainLoop(Timer.java:552)
   - locked <0x000000064c06f530> (a java.util.TaskQueue)
   at java.util.TimerThread.run(Timer.java:505)

"DHNS View Destructor" daemon prio=5 tid=0x00007fa2b1a79800 nid=0xeb07 in Object.wait() [0x0000000119f03000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x0000000638b64278> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.graph.dhns.core.GraphStructure$ViewDestructorThread.run(GraphStructure.java:240)
   - locked <0x0000000638b64278> (a java.lang.Object)

"attribute-event-bus" daemon prio=5 tid=0x00007fa2b192e800 nid=0xea07 in Object.wait() [0x0000000119e00000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00000006399eaab8> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.data.attributes.event.AttributeEventManager.run(AttributeEventManager.java:137)
   - locked <0x00000006399eaab8> (a java.lang.Object)
   at java.lang.Thread.run(Thread.java:724)

"graph-event-bus" daemon prio=5 tid=0x00007fa2b1742800 nid=0xf81b in Object.wait() [0x0000000119cfd000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00000006399eaba0> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.graph.dhns.core.EventManager.run(EventManager.java:134)
   - locked <0x00000006399eaba0> (a java.lang.Object)
   at java.lang.Thread.run(Thread.java:724)

"Timer-0" daemon prio=5 tid=0x00007fa2ab157800 nid=0xe603 in Object.wait() [0x0000000115e84000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d9515a8> (a java.util.TaskQueue)
   at java.lang.Object.wait(Object.java:503)
   at java.util.TimerThread.mainLoop(Timer.java:526)
   - locked <0x000000061d9515a8> (a java.util.TaskQueue)
   at java.util.TimerThread.run(Timer.java:505)

"Dynamic Set Visible Interval Thread" daemon prio=5 tid=0x00007fa2ab001000 nid=0xe503 in Object.wait() [0x0000000115666000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d98fe48> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.dynamic.DynamicControllerImpl$SetVisibleIntervalThread.run(DynamicControllerImpl.java:254)
   - locked <0x000000061d98fe48> (a java.lang.Object)

"Dynamic Model EventDispatchThread" daemon prio=5 tid=0x00007fa2b18cc800 nid=0xa907 in Object.wait() [0x0000000115563000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d98fed0> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at org.gephi.dynamic.DynamicControllerImpl$DynamicModelEventDispatchThread.run(DynamicControllerImpl.java:299)
   - locked <0x000000061d98fed0> (a java.lang.Object)

"DestroyJavaVM" prio=5 tid=0x00007fa2ad859800 nid=0x1703 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"TimerQueue" daemon prio=5 tid=0x00007fa2acbed800 nid=0xdd2f waiting on condition [0x0000000112c40000]
   java.lang.Thread.State: WAITING (parking)
   at sun.misc.Unsafe.park(Native Method)
   - parking to wait for  <0x000000061d764600> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
   at java.util.concurrent.locks.LockSupport.park(LockSupport.java:186)
   at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2043)
   at java.util.concurrent.DelayQueue.take(DelayQueue.java:209)
   at javax.swing.TimerQueue.run(TimerQueue.java:171)
   at java.lang.Thread.run(Thread.java:724)

"Thread-3" daemon prio=5 tid=0x00007fa2acc53800 nid=0xde2f in Object.wait() [0x0000000115460000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d7646c8> (a java.util.LinkedList)
   at java.lang.Object.wait(Object.java:503)
   at java.util.prefs.AbstractPreferences$EventDispatchThread.run(AbstractPreferences.java:1476)
   - locked <0x000000061d7646c8> (a java.util.LinkedList)

"File Watcher" daemon prio=5 tid=0x00007fa2abb69800 nid=0xdc03 waiting on condition [0x0000000112485000]
   java.lang.Thread.State: WAITING (parking)
   at sun.misc.Unsafe.park(Native Method)
   - parking to wait for  <0x000000061d764790> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
   at java.util.concurrent.locks.LockSupport.park(LockSupport.java:186)
   at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2043)
   at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)
   at org.netbeans.modules.masterfs.watcher.macosx.OSXNotifier.nextEvent(OSXNotifier.java:105)
   at org.netbeans.modules.masterfs.providers.Notifier$1.nextEvent(Notifier.java:119)
   at org.netbeans.modules.masterfs.watcher.Watcher$Ext.run(Watcher.java:301)
   at java.lang.Thread.run(Thread.java:724)

"Thread-2" daemon prio=5 tid=0x00007fa2abc66800 nid=0xd52f runnable [0x0000000112256000]
   java.lang.Thread.State: RUNNABLE
   at com.sun.jna.Native.invokeVoid(Native Method)
   at com.sun.jna.Function.invoke(Function.java:328)
   at com.sun.jna.Function.invoke(Function.java:276)
   at com.sun.jna.Library$Handler.invoke(Library.java:216)
   at com.sun.proxy.$Proxy3.CFRunLoopRun(Unknown Source)
   at org.netbeans.modules.masterfs.watcher.macosx.OSXNotifier$1.run(OSXNotifier.java:126)
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
   at java.lang.Thread.run(Thread.java:724)

"AWT-EventQueue-0" prio=5 tid=0x00007fa2aba0c000 nid=0xb803 in Object.wait() [0x000000010e21b000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061da48fc0> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at com.sun.opengl.impl.GLContextLock.lock(GLContextLock.java:73)
   - locked <0x000000061da48fc0> (a java.lang.Object)
   at com.sun.opengl.impl.GLContextImpl.destroy(GLContextImpl.java:203)
   at javax.media.opengl.GLCanvas$DestroyAction.run(GLCanvas.java:471)
   at javax.media.opengl.GLCanvas.removeNotify(GLCanvas.java:320)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at org.netbeans.swing.tabcontrol.TabbedContainer.removeNotify(TabbedContainer.java:960)
   at org.netbeans.core.windows.view.ui.tabcontrol.TabbedAdapter.removeNotify(TabbedAdapter.java:331)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.removeNotify(Container.java:2800)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at javax.swing.JComponent.removeNotify(JComponent.java:4761)
   at java.awt.Container.remove(Container.java:1199)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at java.awt.Container.remove(Container.java:1257)
   - locked <0x000000061d170978> (a java.awt.Component$AWTTreeLock)
   at org.netbeans.core.windows.view.ui.DesktopImpl.setViewComponent(DesktopImpl.java:166)
   at org.netbeans.core.windows.view.ui.DesktopImpl.setSplitRoot(DesktopImpl.java:144)
   at org.netbeans.core.windows.view.ViewHierarchy.setSplitRootIntoDesktop(ViewHierarchy.java:659)
   at org.netbeans.core.windows.view.ViewHierarchy.updateDesktop(ViewHierarchy.java:700)
   at org.netbeans.core.windows.view.DefaultView.changeGUI(DefaultView.java:262)
   at org.netbeans.core.windows.ViewRequestor.dispatchRequest(ViewRequestor.java:273)
   at org.netbeans.core.windows.ViewRequestor.processRequest(ViewRequestor.java:249)
   at org.netbeans.core.windows.ViewRequestor.postRequest(ViewRequestor.java:187)
   at org.netbeans.core.windows.ViewRequestor.scheduleRequest(ViewRequestor.java:127)
   at org.netbeans.core.windows.Central.setEditorAreaConstraints(Central.java:281)
   at org.netbeans.core.windows.WindowManagerImpl.setEditorAreaConstraints(WindowManagerImpl.java:787)
   at org.netbeans.core.windows.PersistenceHandler.load(PersistenceHandler.java:182)
   at org.netbeans.core.windows.WindowSystemImpl.load(WindowSystemImpl.java:81)
   at org.netbeans.core.windows.WindowManagerImpl.switchRole(WindowManagerImpl.java:1884)
   at org.netbeans.core.windows.WindowManagerImpl.setRole(WindowManagerImpl.java:1838)
   at org.netbeans.core.windows.WindowManagerImpl.setRole(WindowManagerImpl.java:1823)
   at org.gephi.perspective.PerspectiveControllerImpl.openAndCloseMembers(PerspectiveControllerImpl.java:164)
   at org.gephi.perspective.PerspectiveControllerImpl.selectPerspective(PerspectiveControllerImpl.java:157)
   at org.gephi.desktop.perspective.BannerComponent$2.actionPerformed(BannerComponent.java:106)
   at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
   at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
   at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
   at javax.swing.JToggleButton$ToggleButtonModel.setPressed(JToggleButton.java:308)
   at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
   at java.awt.Component.processMouseEvent(Component.java:6505)
   at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
   at java.awt.Component.processEvent(Component.java:6270)
   at java.awt.Container.processEvent(Container.java:2229)
   at java.awt.Component.dispatchEventImpl(Component.java:4861)
   at java.awt.Container.dispatchEventImpl(Container.java:2287)
   at java.awt.Component.dispatchEvent(Component.java:4687)
   at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
   at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
   at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
   at java.awt.Container.dispatchEventImpl(Container.java:2273)
   at java.awt.Window.dispatchEventImpl(Window.java:2719)
   at java.awt.Component.dispatchEvent(Component.java:4687)
   at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
   at java.awt.EventQueue.access$200(EventQueue.java:103)
   at java.awt.EventQueue$3.run(EventQueue.java:694)
   at java.awt.EventQueue$3.run(EventQueue.java:692)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
   at java.awt.EventQueue$4.run(EventQueue.java:708)
   at java.awt.EventQueue$4.run(EventQueue.java:706)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
   at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
   at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:158)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
   at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
   at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
   at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

"Java2D Disposer" daemon prio=5 tid=0x00007fa2ab9bc000 nid=0xb703 in Object.wait() [0x000000010e0b1000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6130> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
   - locked <0x000000061d0e6130> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:151)
   at sun.java2d.Disposer.run(Disposer.java:145)
   at java.lang.Thread.run(Thread.java:724)

"Java2D Queue Flusher" daemon prio=5 tid=0x00007fa2ae811800 nid=0xad07 in Object.wait() [0x000000010ce4f000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6170> (a sun.java2d.opengl.OGLRenderQueue$QueueFlusher)
   at sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run(OGLRenderQueue.java:208)
   - locked <0x000000061d0e6170> (a sun.java2d.opengl.OGLRenderQueue$QueueFlusher)

"RequestProcessor queue manager" daemon prio=5 tid=0x00007fa2aa985000 nid=0xa707 in Object.wait() [0x000000010cd4c000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6258> (a java.lang.Class for org.openide.util.RequestProcessor$TickTac)
   at org.openide.util.RequestProcessor$TickTac.obtainFirst(RequestProcessor.java:2249)
   - locked <0x000000061d0e6258> (a java.lang.Class for org.openide.util.RequestProcessor$TickTac)
   at org.openide.util.RequestProcessor$TickTac.run(RequestProcessor.java:2225)

"AWT-Shutdown" prio=5 tid=0x00007fa2ae802800 nid=0x4407 in Object.wait() [0x00000001087cd000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6628> (a java.lang.Object)
   at java.lang.Object.wait(Object.java:503)
   at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:287)
   - locked <0x000000061d0e6628> (a java.lang.Object)
   at java.lang.Thread.run(Thread.java:724)

"AppKit Thread" daemon prio=5 tid=0x00007fa2ab0d8000 nid=0x507 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"CLI Requests Server" daemon prio=5 tid=0x00007fa2ab95e000 nid=0x3f03 runnable [0x000000010847c000]
   java.lang.Thread.State: RUNNABLE
   at java.net.PlainSocketImpl.socketAccept(Native Method)
   at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:398)
   at java.net.ServerSocket.implAccept(ServerSocket.java:530)
   at java.net.ServerSocket.accept(ServerSocket.java:498)
   at org.netbeans.CLIHandler$Server.run(CLIHandler.java:1085)

"Active Reference Queue Daemon" daemon prio=5 tid=0x00007fa2ac84d800 nid=0x3e03 in Object.wait() [0x0000000108379000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e68e8> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
   - locked <0x000000061d0e68e8> (a java.lang.ref.ReferenceQueue$Lock)
   at org.openide.util.lookup.implspi.ActiveQueue$Daemon.run(ActiveQueue.java:180)
   - locked <0x000000061d0e68e8> (a java.lang.ref.ReferenceQueue$Lock)

"Service Thread" daemon prio=5 tid=0x00007fa2ab83d800 nid=0x3c03 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread1" daemon prio=5 tid=0x00007fa2ab83c800 nid=0x3b03 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" daemon prio=5 tid=0x00007fa2ab83c000 nid=0x3a03 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" daemon prio=5 tid=0x00007fa2ab83b000 nid=0x3903 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=5 tid=0x00007fa2ab803000 nid=0x2603 in Object.wait() [0x000000010799e000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e6bd0> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
   - locked <0x000000061d0e6bd0> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:151)
   at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:189)

"Reference Handler" daemon prio=5 tid=0x00007fa2ab802000 nid=0x2503 in Object.wait() [0x000000010789b000]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x000000061d0e62f0> (a java.lang.ref.Reference$Lock)
   at java.lang.Object.wait(Object.java:503)
   at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:133)
   - locked <0x000000061d0e62f0> (a java.lang.ref.Reference$Lock)

"VM Thread" prio=5 tid=0x00007fa2ab051000 nid=0x2403 runnable

"VM Periodic Task Thread" prio=5 tid=0x00007fa2aa80a800 nid=0x3d03 waiting on condition

JNI global references: 1423

Heap
 def new generation   total 592128K, used 27954K [0x000000052e200000, 0x0000000556480000, 0x000000061d0a0000)
  eden space 526336K,   3% used [0x000000052e200000, 0x000000052f5ff7a0, 0x000000054e400000)
  from space 65792K,  11% used [0x0000000552440000, 0x0000000552b8d0b0, 0x0000000556480000)
  to   space 65792K,   0% used [0x000000054e400000, 0x000000054e400000, 0x0000000552440000)
 tenured generation   total 1315748K, used 789446K [0x000000061d0a0000, 0x000000066d589000, 0x00000007fae00000)
   the space 1315748K,  59% used [0x000000061d0a0000, 0x000000064d391aa8, 0x000000064d391c00, 0x000000066d589000)
 compacting perm gen  total 46720K, used 46682K [0x00000007fae00000, 0x00000007fdba0000, 0x0000000800000000)
   the space 46720K,  99% used [0x00000007fae00000, 0x00000007fdb96908, 0x00000007fdb96a00, 0x00000007fdba0000)
No shared spaces configured.

^Z
[1]+  Stopped                 /Applications/Gephi.app/Contents/Resources/gephi/bin/gephi


Edit:

It appears to definitely be an issue with the graph
graphjunkie
 
Posts: 5
Joined: 24 Oct 2013 22:33

Re: Gephi on OS X Mavericks?

Postby ocaoimh » 24 Oct 2013 23:05

Hi,

I installed the java update http://support.apple.com/kb/DL1572?viewlocale=en_US and so far, so good!
ocaoimh
 
Posts: 1
Joined: 22 Jun 2013 15:57

Re: Gephi on OS X Mavericks?

Postby graphjunkie » 24 Oct 2013 23:12

Okay I thought I got it working by doing this;
DONT DO THIS - IT'S A TERRIBLE IDEA. Only posting this work to warn other people not to do it.

1) Download gephi-0.9-SNAPSHOT.dmg from https://github.com/gephi/gephi
2) Delete the ${HOME}/Library/Application Support/gephi/ directory (old prefs make gui go weird)
3) Gephi has a problem updating it's ram so you have to modify your /Applications/Gephi.app/Contents/Resources/gephi/etc/gephi.conf mem limits yourself (with admin rights)
4) files load, graph displays
5) realize theres no plugins or features your used to and cry.

The next thing I'm going to try is editing
PerspectiveControllerImpl_selectedPerspective=overview
/Users/_/Library/Application Support/gephi/0.8.2/dev/config/Preferences.properties
to a different perspective, but unfortunately I don't know the other values it can be yet..
Looking at the source it's referenced here.
https://github.com/gephi/gephi/blob/0.8 ... rImpl.java
graphjunkie
 
Posts: 5
Joined: 24 Oct 2013 22:33

Re: Gephi on OS X Mavericks?

Postby graphjunkie » 24 Oct 2013 23:20

so I found https://github.com/gephi/gephi/tree/0.8 ... op/datalab

took a stab at modifying /Users/_/Library/Application Support/gephi/0.8.2/dev/config/Preferences.properties
to PerspectiveControllerImpl_selectedPerspective=datalab

open up gephi, and at least you can load and manipulate the graph data, seems pretty usable, as long as you don't look at the graph visualization you're golden!
graphjunkie
 
Posts: 5
Joined: 24 Oct 2013 22:33

Re: Gephi on OS X Mavericks?

Postby searain » 25 Oct 2013 09:46

I upgraded to OS X 10.9, and installed Java SE 6. Now I cannot open my gephi project. The message says "Impossible to open this file. It must be a compatible '.gephi' file.
searain
 
Posts: 3
Joined: 25 Oct 2013 09:42

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