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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
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IGV 2.6.3 java.lang.NullPointerException: null on Mac #701

Closed MeHelmy closed 5 years ago

MeHelmy commented 5 years ago

I got java.lang.NullPointerException: null when I try to run IGV 2.6.3

I tried both

Based on issue #651 I also installed OpenJDK 11, but nothing changed.

Using system JDK.
WARNING: package com.sun.java.swing.plaf.windows not in java.desktop
WARNING: package sun.awt.windows not in java.desktop
openjdk version "11.0.4" 2019-07-16
OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.4+11)
OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.4+11, mixed mode)
WARN [2019-09-27T10:50:23,596]  [Globals.java:138] [AWT-EventQueue-0]  Development mode is enabled
INFO [2019-09-27T10:50:23,619]  [DirectoryManager.java:179] [AWT-EventQueue-0]  IGV Directory: /Users/mmahmoud/igv
INFO [2019-09-27T10:50:23,635]  [Main.java:156] [AWT-EventQueue-0]  Startup  IGV Version 2.6.3 08/27/2019 12:03 AM
INFO [2019-09-27T10:50:23,645]  [Main.java:157] [AWT-EventQueue-0]  Java 11.0.4 (build 11.0.4+11) 2019-07-16
INFO [2019-09-27T10:50:23,646]  [Main.java:160] [AWT-EventQueue-0]  Java Vendor: AdoptOpenJDK https://adoptopenjdk.net/
INFO [2019-09-27T10:50:23,647]  [Main.java:162] [AWT-EventQueue-0]  JVM: OpenJDK 64-Bit Server VM AdoptOpenJDK
INFO [2019-09-27T10:50:23,647]  [DirectoryManager.java:84] [AWT-EventQueue-0]  Fetching user directory...
INFO [2019-09-27T10:50:23,712]  [Main.java:165] [AWT-EventQueue-0]  Default User Directory: /Users/mmahmoud
INFO [2019-09-27T10:50:23,713]  [Main.java:166] [AWT-EventQueue-0]  OS: Mac OS X 10.14.5 x86_64
ERROR [2019-09-27T10:50:23,743]  [DefaultExceptionHandler.java:49] [AWT-EventQueue-0]  Unhandled exception
java.lang.NullPointerException: null
    at java.awt.Window.init(Window.java:509) ~[?:?]
    at java.awt.Window.<init>(Window.java:549) ~[?:?]
    at java.awt.Frame.<init>(Frame.java:423) ~[?:?]
    at java.awt.Frame.<init>(Frame.java:388) ~[?:?]
    at javax.swing.JFrame.<init>(JFrame.java:180) ~[?:?]
    at org.broad.igv.ui.Main$1.run(Main.java:107) ~[igv.jar:?]
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313) ~[?:?]
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770) ~[?:?]
    at java.awt.EventQueue$4.run(EventQueue.java:721) ~[?:?]
    at java.awt.EventQueue$4.run(EventQueue.java:715) ~[?:?]
    at java.security.AccessController.doPrivileged(Native Method) ~[?:?]
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) ~[?:?]
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:740) ~[?:?]
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) [?:?]
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) [?:?]
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) [?:?]
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) [?:?]
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [?:?]
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:90) [?:?]
INFO [2019-09-27T10:50:24,855]  [ShutdownThread.java:46] [Thread-1]  Shutting down
jrobinso commented 5 years ago

This is the first report of this we have received, and I can't reproduce it. We all use Macs.

Could you try the snapshot version and see if the problem persists? We don't provide a signed mac app for the snapshot, you'll need to unzip and run from the command line. Thanks.

jrobinso commented 5 years ago

Sorry forgot the link https://software.broadinstitute.org/software/igv/download_snapshot

MeHelmy commented 5 years ago

Sorry for the late answer, I downloaded it .

to start ./igv.sh

Error

echo Using bundled JDK.
WARNING: package com.sun.java.swing.plaf.windows not in java.desktop
WARNING: package sun.awt.windows not in java.desktop
openjdk version "11.0.2" 2019-01-15
OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.2+9)
OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.2+9, mixed mode)
WARN [2019-10-01T17:33:39,427]  [Globals.java:139] [AWT-EventQueue-0]  Development mode is enabled
INFO [2019-10-01T17:33:39,443]  [DirectoryManager.java:179] [AWT-EventQueue-0]  IGV Directory: /Users/mmahmoud/igv
INFO [2019-10-01T17:33:39,457]  [Main.java:150] [AWT-EventQueue-0]  Startup  IGV Version snapshot 09/26/2019 08:12 PM
INFO [2019-10-01T17:33:39,466]  [Main.java:151] [AWT-EventQueue-0]  Java 11.0.2 (build 11.0.2+9) 2019-01-15
INFO [2019-10-01T17:33:39,467]  [Main.java:154] [AWT-EventQueue-0]  Java Vendor: AdoptOpenJDK https://adoptopenjdk.net/
INFO [2019-10-01T17:33:39,467]  [Main.java:156] [AWT-EventQueue-0]  JVM: OpenJDK 64-Bit Server VM AdoptOpenJDK
INFO [2019-10-01T17:33:39,468]  [DirectoryManager.java:84] [AWT-EventQueue-0]  Fetching user directory...
INFO [2019-10-01T17:33:39,532]  [Main.java:159] [AWT-EventQueue-0]  Default User Directory: /Users/mmahmoud
INFO [2019-10-01T17:33:39,532]  [Main.java:160] [AWT-EventQueue-0]  OS: Mac OS X 10.14.5 x86_64
ERROR [2019-10-01T17:33:39,552]  [DefaultExceptionHandler.java:49] [AWT-EventQueue-0]  Unhandled exception
java.lang.NullPointerException: null
    at java.awt.Window.init(Unknown Source) ~[?:?]
    at java.awt.Window.<init>(Unknown Source) ~[?:?]
    at java.awt.Frame.<init>(Unknown Source) ~[?:?]
    at java.awt.Frame.<init>(Unknown Source) ~[?:?]
    at javax.swing.JFrame.<init>(Unknown Source) ~[?:?]
    at org.broad.igv.ui.Main.lambda$main$0(Main.java:102) ~[igv.jar:?]
    at java.awt.event.InvocationEvent.dispatch(Unknown Source) ~[?:?]
    at java.awt.EventQueue.dispatchEventImpl(Unknown Source) ~[?:?]
    at java.awt.EventQueue$4.run(Unknown Source) ~[?:?]
    at java.awt.EventQueue$4.run(Unknown Source) ~[?:?]
    at java.security.AccessController.doPrivileged(Native Method) ~[?:?]
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) ~[?:?]
    at java.awt.EventQueue.dispatchEvent(Unknown Source) ~[?:?]
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [?:?]
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [?:?]
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [?:?]
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:?]
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:?]
    at java.awt.EventDispatchThread.run(Unknown Source) [?:?]
INFO [2019-10-01T17:33:40,687]  [ShutdownThread.java:46] [Thread-1]  Shutting down
jrobinso commented 5 years ago

I'm not really sure, note the error is in the java awt, not our application code. I haven't seen this before. Could you try the mac bundle (the app).

On Tue, Oct 1, 2019 at 3:34 PM Medhat notifications@github.com wrote:

Sorry for the late answer, I downloaded it .

to start ./igv.sh

Error

echo Using bundled JDK. WARNING: package com.sun.java.swing.plaf.windows not in java.desktop WARNING: package sun.awt.windows not in java.desktop openjdk version "11.0.2" 2019-01-15 OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.2+9) OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.2+9, mixed mode) WARN [2019-10-01T17:33:39,427] [Globals.java:139] [AWT-EventQueue-0] Development mode is enabled INFO [2019-10-01T17:33:39,443] [DirectoryManager.java:179] [AWT-EventQueue-0] IGV Directory: /Users/mmahmoud/igv INFO [2019-10-01T17:33:39,457] [Main.java:150] [AWT-EventQueue-0] Startup IGV Version snapshot 09/26/2019 08:12 PM INFO [2019-10-01T17:33:39,466] [Main.java:151] [AWT-EventQueue-0] Java 11.0.2 (build 11.0.2+9) 2019-01-15 INFO [2019-10-01T17:33:39,467] [Main.java:154] [AWT-EventQueue-0] Java Vendor: AdoptOpenJDK https://adoptopenjdk.net/ INFO [2019-10-01T17:33:39,467] [Main.java:156] [AWT-EventQueue-0] JVM: OpenJDK 64-Bit Server VM AdoptOpenJDK INFO [2019-10-01T17:33:39,468] [DirectoryManager.java:84] [AWT-EventQueue-0] Fetching user directory... INFO [2019-10-01T17:33:39,532] [Main.java:159] [AWT-EventQueue-0] Default User Directory: /Users/mmahmoud INFO [2019-10-01T17:33:39,532] [Main.java:160] [AWT-EventQueue-0] OS: Mac OS X 10.14.5 x86_64 ERROR [2019-10-01T17:33:39,552] [DefaultExceptionHandler.java:49] [AWT-EventQueue-0] Unhandled exception java.lang.NullPointerException: null at java.awt.Window.init(Unknown Source) ~[?:?] at java.awt.Window.(Unknown Source) ~[?:?] at java.awt.Frame.(Unknown Source) ~[?:?] at java.awt.Frame.(Unknown Source) ~[?:?] at javax.swing.JFrame.(Unknown Source) ~[?:?] at org.broad.igv.ui.Main.lambda$main$0(Main.java:102) ~[igv.jar:?] at java.awt.event.InvocationEvent.dispatch(Unknown Source) ~[?:?] at java.awt.EventQueue.dispatchEventImpl(Unknown Source) ~[?:?] at java.awt.EventQueue$4.run(Unknown Source) ~[?:?] at java.awt.EventQueue$4.run(Unknown Source) ~[?:?] at java.security.AccessController.doPrivileged(Native Method) ~[?:?] at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) ~[?:?] at java.awt.EventQueue.dispatchEvent(Unknown Source) ~[?:?] at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [?:?] at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [?:?] at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [?:?] at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:?] at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:?] at java.awt.EventDispatchThread.run(Unknown Source) [?:?] INFO [2019-10-01T17:33:40,687] [ShutdownThread.java:46] [Thread-1] Shutting down

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MeHelmy commented 5 years ago

Thanks for your continuous help.

I identified the issue. it has no relation to the code at all, and the error is not informative.

The Issue is when you connect mac to an external screen and close the led, IGV will not work (I see how it is sound). so the solution is to open mac led, only then the IGV will work.

More could be found here: https://github.com/oracle/visualvm/issues/84#issuecomment-474830113

Thanks, Medhat

jrobinso commented 5 years ago

OK, thanks for the link. There's nothing we can do about that obviously, hopefully they fix it soon.

On Wed, Oct 2, 2019 at 8:57 AM Medhat notifications@github.com wrote:

Thanks for your continuous help.

I identified the issue. it has no relation to the code at all, and the error is not informative.

The Issue is when you connect mac to an external screen and close the led IGV will not work (I see how it is sound). so the solution is to open mac led, only then the IGV will work.

More could be found here: oracle/visualvm#84 (comment) https://github.com/oracle/visualvm/issues/84#issuecomment-474830113

Thanks, Medhat

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/701?email_source=notifications&email_token=AAHD2HBQCTWWRGI7VKSXUVDQMTAFRA5CNFSM4I3ID6YKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAFIKQA#issuecomment-537560384, or mute the thread https://github.com/notifications/unsubscribe-auth/AAHD2HAKXK5I4RSUCFU72MLQMTAFRANCNFSM4I3ID6YA .