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The mitochondrial workbench
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Mitobench-1.4-beta.jar throws class not found exception: JavaFX #77

Closed subwaystation closed 4 years ago

subwaystation commented 5 years ago

Hi @JudithNeukamm I tried to run mitoBench, but I ran into the following issue:

[heumos@wave Downloads]$ java -jar MitoBench-1.4-beta.jar 
Exception in thread "Thread-0" java.lang.NoClassDefFoundError: javafx/application/Application
    at java.base/java.lang.ClassLoader.defineClass1(Native Method)
    at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1016)
    at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:151)
    at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:802)
    at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:700)
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:623)
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
    at MitoBenchStarter.lambda$main$0(MitoBenchStarter.java:17)
    at java.base/java.lang.Thread.run(Thread.java:835)
Caused by: java.lang.ClassNotFoundException: javafx.application.Application
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:583)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
    ... 11 more

Even after installing java-openjfx, the error persists.

Any ideas?

JudithNeukamm commented 5 years ago

Hi Simon, which java version are you using? It works fine with java8, as far as I know, the installation of JavaFX with higher java version is a bit more tricky.

Best. Judith

subwaystation commented 5 years ago

Hi Judith, I am using Java12:

heumos@wave ~/g/GenGraph> java --version
openjdk 12.0.2 2019-07-16
OpenJDK Runtime Environment (build 12.0.2+10)
OpenJDK 64-Bit Server VM (build 12.0.2+10, mixed mode)

I guess you build Mitobench with Java8 in mind. There JavaFX is still integrated into the JDK. However, I think since Java9 or so?! it is not part of the JDK anymore. So you need to ship it directly with your application, if I understood everything correctly: https://stackoverflow.com/questions/16868446/javafx-exception-in-thread-main-java-lang-noclassdeffounderror-javafx-applica

What do you think? Best, Simon

JudithNeukamm commented 5 years ago

That's definitely a point of my todo list, but not implemented at the moment. Until it's done, you might have to run mitoBench with java8.

subwaystation commented 5 years ago

I see. Thanks!

subwaystation commented 4 years ago

Hi Judith,

now it works!

However:


java --module-path javafx-sdk-11.0.2/lib  
--add-modules=javafx.controls -jar MitoBench-1.6-beta.jar
Exception in thread "JavaFX Application Thread"  
java.lang.NoClassDefFoundError: javafx/scene/web/WebView
    at view.menus.HelpMenu.lambda$add$1(HelpMenu.java:48)
    at  
javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at  
javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at  
javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at  
javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at  
javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at  
javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
    at javafx.base/javafx.event.Event.fireEvent(Event.java:198)
    at javafx.controls/javafx.scene.control.MenuItem.fire(MenuItem.java:465)
    at  
javafx.controls/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1380)
    at  
javafx.controls/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(ContextMenuContent.java:1333)
    at  
javafx.base/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
    at  
javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
    at  
javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at  
javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at  
javafx.base/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at  
javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at  
javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at  
javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at  
javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at  
javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at  
javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at  
javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at  
javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at  
javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.base/javafx.event.Event.fireEvent(Event.java:198)
    at  
javafx.graphics/javafx.scene.Scene$MouseHandler.process(Scene.java:3851)
    at  
javafx.graphics/javafx.scene.Scene$MouseHandler.access$1200(Scene.java:3579)
    at javafx.graphics/javafx.scene.Scene.processMouseEvent(Scene.java:1849)
    at  
javafx.graphics/javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2588)
    at  
javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:397)
    at  
javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:295)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at  
javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:434)
    at  
javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:390)
    at  
javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:433)
    at javafx.graphics/com.sun.glass.ui.View.handleMouseEvent(View.java:556)
    at javafx.graphics/com.sun.glass.ui.View.notifyMouse(View.java:942)
    at  
javafx.graphics/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native  
Method)
    at  
javafx.graphics/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(GtkApplication.java:277)
    at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.ClassNotFoundException: javafx.scene.web.WebView
    at  
java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
    at  
java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
    ... 43 more
Exception in thread "JavaFX Application Thread"  
java.lang.NoClassDefFoundError: javafx/scene/web/WebView
    at view.menus.HelpMenu.lambda$add$1(HelpMenu.java:48)
    at  
javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at  
javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at  
javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at  
javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at  
javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at  
javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
    at javafx.base/javafx.event.Event.fireEvent(Event.java:198)
    at javafx.controls/javafx.scene.control.MenuItem.fire(MenuItem.java:465)
    at  
javafx.controls/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1380)
    at  
javafx.controls/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(ContextMenuContent.java:1333)
    at  
javafx.base/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
    at  
javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
    at  
javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at  
javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at  
javafx.base/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at  
javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at  
javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at  
javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at  
javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at  
javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at  
javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at  
javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at  
javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at  
javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.base/javafx.event.Event.fireEvent(Event.java:198)
    at  
javafx.graphics/javafx.scene.Scene$MouseHandler.process(Scene.java:3851)
    at  
javafx.graphics/javafx.scene.Scene$MouseHandler.access$1200(Scene.java:3579)
    at javafx.graphics/javafx.scene.Scene.processMouseEvent(Scene.java:1849)
    at  
javafx.graphics/javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2588)
    at  
javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:397)
    at  
javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:295)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at  
javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:434)
    at  
javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:390)
    at  
javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:433)
    at javafx.graphics/com.sun.glass.ui.View.handleMouseEvent(View.java:556)
    at javafx.graphics/com.sun.glass.ui.View.notifyMouse(View.java:942)
    at  
javafx.graphics/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native  
Method)
    at  
javafx.graphics/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(GtkApplication.java:277)
    at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.ClassNotFoundException: javafx.scene.web.WebView
    at  
java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
    at  
java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
    ... 43 more

When I click on Help + About Mitobench.

Best,

JudithNeukamm commented 4 years ago

I know. That's why I deleted my last post ;)

subwaystation commented 4 years ago

Ups, did not see that :P

JudithNeukamm commented 4 years ago

mitoBench is now updated to Java11 and will be available with the next release. I am closing this issue, but please let me know if it does not work.

nieselt commented 4 years ago

Hi Judith,

ich habe es gerade mal gestartet. Es funktioniert, aber das kommt als Meldung auf der Console:

java -jar mitoBench-1.7-beta.jar 2020-11-11 16:22:20.723 java[43056:13329524] unrecognized type is 4294967295 2020-11-11 16:22:20.723 java[43056:13329524] *** Assertion failure in -[NSEvent _initWithCGEvent:eventRef:], /BuildRoot/Library/Caches/com.apple.xbs/Sources/AppKit/AppKit-1671.60.109/AppKit.subproj/NSEvent.m:1977

Die Version under releases stammt vom 16.8. Kann das sein?

VG,

Kay

On 11. Nov 2020, at 16:15, Judith Neukamm notifications@github.com wrote:

mitoBench is now updated to Java11 and will be available with the next release. I am closing this issue, but please let me know if it does not work.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/mitobench/mitoBench/issues/77#issuecomment-725475541, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABP6RYOY6DPEVGSFRPCLR3DSPKTC5ANCNFSM4IIQPEXQ.

JudithNeukamm commented 4 years ago

Hi Kay, also die Version 1.7-beta läuft nur unter Java8. Kam die Fehlermeldung direkt nach dem Starten, oder nachdem du etwas geklickt hast? Grüsse, Judith

JudithNeukamm commented 4 years ago

Und die Release, die unter Java11 läuft, kommt erst noch.

Der Fehler scheint MacOS spezifisch zu sein, ich werd mich mal schlau machen.

nieselt commented 4 years ago

Des wegen frage ich nach, da du ja rumgeschickt hattest, dass es jetzt ein java11-release gibt, aber es nur java8 bislang im git ist.

Diese Version: Ja es läuft unter mac unter Java 8 und wirft diese Meldungen, wenn man was klickt.

VG,

Kay

On 11. Nov 2020, at 16:38, Judith Neukamm notifications@github.com wrote:

Und die Release, die unter Java11 läuft, kommt erst noch.

Der Fehler scheint MacOS spezifisch zu sein, ich werd mich mal schlau machen.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/mitobench/mitoBench/issues/77#issuecomment-725493693, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABP6RYL3MP4QSU65EHCRLODSPKVY7ANCNFSM4IIQPEXQ.