Error while open iGV: [DefaultExceptionHandler.java:49] [AWT-EventQueue-0] Unhandled exception

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coronafy

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Apr 1, 2018, 3:23:54 AM4/1/18
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I cannot open iGV after upgrade my Mac OS. Have already updated to the latest version of JKD, it showed following error message while using command line. Any idea how to solve it? Thanks!

ERROR [2018-04-01 15:17:16,175]  [DefaultExceptionHandler.java:49] [AWT-EventQueue-0]  Unhandled exception

java.lang.NoClassDefFoundError: com/sun/java/swing/plaf/windows/WindowsLookAndFeel

at com.jidesoft.plaf.LookAndFeelFactory.installJideExtension(LookAndFeelFactory.java:848)

at com.jidesoft.plaf.LookAndFeelFactory.installJideExtension(LookAndFeelFactory.java:633)

at com.jidesoft.plaf.LookAndFeelFactory.installJideExtension(LookAndFeelFactory.java:598)

at org.broad.igv.ui.Main.initializeLookAndFeel(Main.java:324)

at org.broad.igv.ui.Main.open(Main.java:265)

at org.broad.igv.ui.Main$1.run(Main.java:108)

at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)

at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)

at java.desktop/java.awt.EventQueue.access$600(EventQueue.java:97)

at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)

at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)

at java.base/java.security.AccessController.doPrivileged(Native Method)

at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)

at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)

at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)

at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)

at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)

at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)

at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)

at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

Caused by: java.lang.ClassNotFoundException: com.sun.java.swing.plaf.windows.WindowsLookAndFeel

at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)

at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:190)

at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:499)

... 20 more

java.io.FileNotFoundException: File not found: https://dn7ywbm9isq8j.cloudfront.net/app/oauth_native.json

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:775)

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:611)

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:607)

at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:148)

at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:141)

at org.broad.igv.ga4gh.OAuthUtils.fetchOauthProperties(OAuthUtils.java:135)

at org.broad.igv.ga4gh.OAuthUtils.<init>(OAuthUtils.java:123)

at org.broad.igv.ga4gh.OAuthUtils.<clinit>(OAuthUtils.java:104)

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:628)

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:611)

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:607)

at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:148)

at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:141)

at org.broad.igv.ui.Main.lambda$checkVersion$0(Main.java:189)

at java.base/java.lang.Thread.run(Thread.java:844)

David Eby

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Apr 1, 2018, 10:32:10 PM4/1/18
to igv-help
IGV is not (yet) compatible with Java 9+.  We recommend sticking to Java 8 for now.

We're working on it but it's non-trivial.

Regards,
David

Mita Tran

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Aug 29, 2018, 10:56:42 PM8/29/18
to igv-help
Dear all,

I also got the same problem in Java 8 on Win 10.

C:\Program Files\IGV_2.4.14\lib>java -Xmx1500m -jar igv.jar
WARN [2018-08-30T10:33:40,986]  [Globals.java:138] [AWT-EventQueue-0]  Development mode is enabled
INFO [2018-08-30T10:33:41,018]  [DirectoryManager.java:84] [AWT-EventQueue-0]  Fetching user directory...
INFO [2018-08-30T10:33:41,042]  [DirectoryManager.java:179] [AWT-EventQueue-0]  IGV Directory: C:\Users\mitaf\igv
INFO [2018-08-30T10:33:41,058]  [Main.java:155] [AWT-EventQueue-0]  Startup  IGV Version 2.4.14 08/14/2018 04:19 PM
INFO [2018-08-30T10:33:41,058]  [Main.java:156] [AWT-EventQueue-0]  Java 1.8.0_181
INFO [2018-08-30T10:33:41,058]  [Main.java:157] [AWT-EventQueue-0]  Default User Directory: C:\Users\mitaf\Documents
INFO [2018-08-30T10:33:41,058]  [Main.java:158] [AWT-EventQueue-0]  OS: Windows 10


ERROR [2018-08-30T10:33:46,980]  [DefaultExceptionHandler.java:49] [AWT-EventQueue-0]  Unhandled exception
java.lang.IllegalArgumentException: port out of range:-1
        at java.net.InetSocketAddress.checkPort(Unknown Source) ~[?:1.8.0_181]
        at java.net.InetSocketAddress.<init>(Unknown Source) ~[?:1.8.0_181]
        at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:743) ~[igv.jar:?]
        at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:675) ~[igv.jar:?]
        at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:671) ~[igv.jar:?]
        at org.broad.igv.util.HttpUtils.getContentsAsGzippedString(HttpUtils.java:203) ~[igv.jar:?]
        at org.broad.igv.ga4gh.OAuthUtils.fetchOauthProperties(OAuthUtils.java:112) ~[igv.jar:?]
        at org.broad.igv.ga4gh.OAuthUtils.<init>(OAuthUtils.java:103) ~[igv.jar:?]
        at org.broad.igv.ga4gh.OAuthUtils.getInstance(OAuthUtils.java:95) ~[igv.jar:?]
        at org.broad.igv.ui.IGVMenuBar.createGoogleMenu(IGVMenuBar.java:1063) ~[igv.jar:?]
        at org.broad.igv.ui.IGVMenuBar.createMenus(IGVMenuBar.java:187) ~[igv.jar:?]
        at org.broad.igv.ui.IGVMenuBar.<init>(IGVMenuBar.java:153) ~[igv.jar:?]
        at org.broad.igv.ui.IGVMenuBar.lambda$createInstance$1(IGVMenuBar.java:140) ~[igv.jar:?]
        at org.broad.igv.ui.util.UIUtilities.invokeAndWaitOnEventThread(UIUtilities.java:166) ~[igv.jar:?]
        at org.broad.igv.ui.IGVMenuBar.createInstance(IGVMenuBar.java:140) ~[igv.jar:?]
        at org.broad.igv.ui.IGV.<init>(IGV.java:259) ~[igv.jar:?]
        at org.broad.igv.ui.IGV.createInstance(IGV.java:160) ~[igv.jar:?]
        at org.broad.igv.ui.Main.open(Main.java:285) ~[igv.jar:?]
        at org.broad.igv.ui.Main$1.run(Main.java:109) ~[igv.jar:?]
        at java.awt.event.InvocationEvent.dispatch(Unknown Source) ~[?:1.8.0_181]
        at java.awt.EventQueue.dispatchEventImpl(Unknown Source) ~[?:1.8.0_181]
        at java.awt.EventQueue.access$500(Unknown Source) ~[?:1.8.0_181]
        at java.awt.EventQueue$3.run(Unknown Source) ~[?:1.8.0_181]
        at java.awt.EventQueue$3.run(Unknown Source) ~[?:1.8.0_181]
        at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_181]
        at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) ~[?:1.8.0_181]
        at java.awt.EventQueue.dispatchEvent(Unknown Source) ~[?:1.8.0_181]
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [?:1.8.0_181]
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [?:1.8.0_181]
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [?:1.8.0_181]
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:1.8.0_181]
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:1.8.0_181]
        at java.awt.EventDispatchThread.run(Unknown Source) [?:1.8.0_181]

James Robinson

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Aug 29, 2018, 11:15:17 PM8/29/18
to igv-help
Hi,

This is actually not the same problem.  There is something unusual about your network environment,  unusual in the sense that this is the first report of this error and I can't reproduce it.   Are you using a proxy?   Could you share your prefs.properties files, located in the "igv" folder in your home directory?   You can email it to igv-...@broadinstitute.org if you don't want to post it here.



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James Robinson

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Aug 29, 2018, 11:54:31 PM8/29/18
to igv-help
I see you sent an email to igv-team,  but you did not attach your prefs.properties file.
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