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Bugzilla – Bug 535 |
[cannot create fiji update site] |
Last modified: 2012-12-06 00:00:38 CST |
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NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug. The Fiji project now uses GitHub Issues for issue tracking. Please file all new issues there. |
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This is what I did to try to reproduce: - go to advanced mode in the updater - click on "Manage Update Sites" - check "For uploading" - click "Add" - fill in the values like this: Name: Hello URL: http://127.0.0.1/~<user>/123/ SSH host: <user>@127.0.0.1 Upload directory: public_html/123/ - click "Okay" It did indeed ask me whether I want to initialize the update site and it worked without problems... Could you start Fiji from a command line and hit Ctrl+\ in the command line window when the freeze happens? This will print a thread dump to the Terminal which might give us a clue as to the problem.Created attachment 82 updater frozen after entering passwordHi Johannes, Thanks for looking into this. Here is the thread dump if it can help. Let me know if there is anything I can test. Sincerely, Jerome Last login: Tue Dec 4 10:01:28 on ttys000 MacBook-Air-de-Jerome:Applications jerome$ pwd /Users/jerome/Applications MacBook-Air-de-Jerome:Applications jerome$ cd /Applications/Fiji.app/ MacBook-Air-de-Jerome:Fiji.app jerome$ Contents/MacOS/ImageJ-macosx 'images/icon.png' from update site 'Fiji' shadows the one from update site 'ImageJ' 'images/icon-flat.png' from update site 'Fiji' shadows the one from update site 'ImageJ' 'jars/bsh.jar' from update site 'Fiji' shadows the one from update site 'ImageJ' 'jars/rsyntaxtextarea.jar' from update site 'Fiji' shadows the one from update site 'ImageJ' Found 293 plugins. Created service: imagej.thread.DefaultThreadService Created service: imagej.event.DefaultEventService Created service: imagej.plugin.DefaultPluginService Found 3 upload mechanisms. log4j:WARN No appenders could be found for logger (org.bushe.swing.event.EventService). log4j:WARN Please initialize the log4j system properly. launching command date --utc +%Y%m%d%H%M%S date: illegal option -- - usage: date [-jnu] [-d dst] [-r seconds] [-t west] [-v[+|-]val[ymwdHMS]] ... [-f fmt date | [[[mm]dd]HH]MM[[cc]yy][.ss]] [+format] ^\2012-12-05 20:12:26 Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.12-b01-434 mixed mode): "Connect thread ftp-ibmp.u-strasbg.fr session" prio=6 tid=10f953800 nid=0x114f9a000 runnable [114f99000] java.lang.Thread.State: RUNNABLE at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:129) at com.jcraft.jsch.IO.getByte(IO.java:82) at com.jcraft.jsch.Session.read(Session.java:811) at com.jcraft.jsch.Session.run(Session.java:1195) at java.lang.Thread.run(Thread.java:680) "TimerQueue" daemon prio=5 tid=118831800 nid=0x11573e000 in Object.wait() [11573d000] java.lang.Thread.State: TIMED_WAITING (on object monitor) at java.lang.Object.wait(Native Method) at javax.swing.TimerQueue.run(TimerQueue.java:232) - locked <77b8f4b10> (a javax.swing.TimerQueue) at java.lang.Thread.run(Thread.java:680) "Timer-0" daemon prio=5 tid=10579a000 nid=0x11509d000 in Object.wait() [11509c000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) - waiting on <77b98b620> (a java.util.TaskQueue) at java.lang.Object.wait(Object.java:485) at java.util.TimerThread.mainLoop(Timer.java:483) - locked <77b98b620> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462) "DestroyJavaVM" prio=5 tid=10f9f8000 nid=0x101e06000 waiting on condition [00000000] java.lang.Thread.State: RUNNABLE "AWT-EventQueue-0" prio=6 tid=1051ed000 nid=0x112d9d000 runnable [112d9a000] java.lang.Thread.State: RUNNABLE at imagej.updater.ssh.SSHFileUploader.readNumber(SSHFileUploader.java:280) at imagej.updater.ssh.SSHFileUploader.upload(SSHFileUploader.java:103) - locked <776eed0f0> (a imagej.updater.ssh.SSHFileUploader) at imagej.updater.core.FilesUploader.upload(FilesUploader.java:193) at imagej.updater.gui.UpdaterFrame.initializeUpdateSite(UpdaterFrame.java:869) at imagej.updater.gui.SitesDialog$SiteDialog.initializeUpdateSite(SitesDialog.java:377) at imagej.updater.gui.SitesDialog$SiteDialog.actionPerformed(SitesDialog.java:413) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) at java.awt.Component.processMouseEvent(Component.java:6382) at javax.swing.JComponent.processMouseEvent(JComponent.java:3275) at java.awt.Component.processEvent(Component.java:6147) at java.awt.Container.processEvent(Container.java:2083) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2141) at java.awt.Component.dispatchEvent(Component.java:4572) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4280) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210) at java.awt.Container.dispatchEventImpl(Container.java:2127) at java.awt.Window.dispatchEventImpl(Window.java:2489) at java.awt.Component.dispatchEvent(Component.java:4572) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:704) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:663) at java.awt.EventQueue$2.run(EventQueue.java:661) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$3.run(EventQueue.java:677) at java.awt.EventQueue$3.run(EventQueue.java:675) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:674) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) "Java2D Disposer" daemon prio=10 tid=10f8c6800 nid=0x112bf5000 in Object.wait() [112bf4000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) - waiting on <77b6a8d68> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118) - locked <77b6a8d68> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134) at sun.java2d.Disposer.run(Disposer.java:127) at java.lang.Thread.run(Thread.java:680) "GC Daemon" daemon prio=2 tid=1051ec000 nid=0x112898000 in Object.wait() [112897000] java.lang.Thread.State: TIMED_WAITING (on object monitor) at java.lang.Object.wait(Native Method) - waiting on <77b3e8a78> (a sun.misc.GC$LatencyLock) at sun.misc.GC$Daemon.run(GC.java:100) - locked <77b3e8a78> (a sun.misc.GC$LatencyLock) "RMI Reaper" prio=5 tid=10519c000 nid=0x112795000 in Object.wait() [112794000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) - waiting on <77b3e7918> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118) - locked <77b3e7918> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134) at sun.rmi.transport.ObjectTable$Reaper.run(ObjectTable.java:333) at java.lang.Thread.run(Thread.java:680) "RMI TCP Accept-0" daemon prio=5 tid=10519b800 nid=0x112692000 runnable [112691000] java.lang.Thread.State: RUNNABLE at java.net.PlainSocketImpl.socketAccept(Native Method) at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:408) - locked <77b3e79a0> (a java.net.SocksSocketImpl) at java.net.ServerSocket.implAccept(ServerSocket.java:462) at java.net.ServerSocket.accept(ServerSocket.java:430) at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.executeAcceptLoop(TCPTransport.java:369) at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.run(TCPTransport.java:341) at java.lang.Thread.run(Thread.java:680) "AWT-Shutdown" prio=5 tid=1053a1000 nid=0x110744000 in Object.wait() [110743000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) - waiting on <77b3bb990> (a java.lang.Object) at java.lang.Object.wait(Object.java:485) at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:265) - locked <77b3bb990> (a java.lang.Object) at java.lang.Thread.run(Thread.java:680) "AWT-AppKit" daemon prio=5 tid=10539d800 nid=0x7fff7b2e4180 runnable [00000000] java.lang.Thread.State: RUNNABLE "Low Memory Detector" daemon prio=5 tid=10f81a800 nid=0x10f794000 runnable [00000000] java.lang.Thread.State: RUNNABLE "C2 CompilerThread1" daemon prio=9 tid=10f819800 nid=0x10f691000 waiting on condition [00000000] java.lang.Thread.State: RUNNABLE "C2 CompilerThread0" daemon prio=9 tid=10f819000 nid=0x10f58e000 waiting on condition [00000000] java.lang.Thread.State: RUNNABLE "Signal Dispatcher" daemon prio=9 tid=10f818000 nid=0x10f48b000 waiting on condition [00000000] java.lang.Thread.State: RUNNABLE "Surrogate Locker Thread (Concurrent GC)" daemon prio=5 tid=10f817000 nid=0x10f388000 waiting on condition [00000000] java.lang.Thread.State: RUNNABLE "Finalizer" daemon prio=8 tid=1050fd000 nid=0x10f285000 in Object.wait() [10f284000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) - waiting on <77b3eb1a0> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118) - locked <77b3eb1a0> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134) at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159) "Reference Handler" daemon prio=10 tid=1050fc800 nid=0x10f182000 in Object.wait() [10f181000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) - waiting on <77b3e8f88> (a java.lang.ref.Reference$Lock) at java.lang.Object.wait(Object.java:485) at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116) - locked <77b3e8f88> (a java.lang.ref.Reference$Lock) "VM Thread" prio=9 tid=1050f7800 nid=0x10f07f000 runnable "Gang worker#0 (Parallel GC Threads)" prio=9 tid=105000800 nid=0x104f01000 runnable "Gang worker#1 (Parallel GC Threads)" prio=9 tid=105001000 nid=0x109102000 runnable "Gang worker#2 (Parallel GC Threads)" prio=9 tid=105002000 nid=0x109205000 runnable "Gang worker#3 (Parallel GC Threads)" prio=9 tid=105002800 nid=0x109308000 runnable "Concurrent Mark-Sweep GC Thread" prio=9 tid=10507d800 nid=0x10ed8b000 runnable "VM Periodic Task Thread" prio=10 tid=10f82c000 nid=0x110101000 waiting on condition "Exception Catcher Thread" prio=10 tid=105801800 nid=0x101f3d000 runnable JNI global references: 6374 Heap par new generation total 19136K, used 4905K [775c00000, 7770c0000, 77af30000) eden space 17024K, 16% used [775c00000, 775eba778, 776ca0000) from space 2112K, 100% used [776eb0000, 7770c0000, 7770c0000) to space 2112K, 0% used [776ca0000, 776ca0000, 776eb0000) concurrent mark-sweep generation total 63872K, used 13199K [77af30000, 77ed90000, 7f8000000) concurrent-mark-sweep perm gen total 131072K, used 31641K [7f8000000, 800000000, 800000000)Created attachment 83 Tentative fix for 'date --utc' not being understood by MacOSX