Skip to content

Installation issues for version 4.3.1 #5258

Closed
@sebastian-brunner

Description

@sebastian-brunner

I try to use the newest Jabref version, as I get these freezes you reported at (http://help.jabref.org/en/Installation#freezes-when-running-jabref). However, I am continuously getting the following error:

Error: Could not find or load main class org.jabref.JabRefMain
Caused by: java.lang.NoClassDefFoundError: javafx/application/Application

I use Ubuntu 18.04 and try with Jabref version 4.3.1 from https://www.fosshub.com/JabRef.html

So far I tried:

Your install instructions: http://help.jabref.org/en/Installation#jabref-4x-1
They fail at line: Install: sudo apt-get install oracle-java8-installer

You claim at https://github.com/JabRef/jabref#installation that jabref is supporting Java 11 or higher, however in your installation instructions (http://help.jabref.org/en/Installation#jabref-4x-1) you say it does not support java 11.

Nevertheless, I tried java 11 using the default-jdk package including openjfx which was reported to work: http://discourse.jabref.org/t/jabref-4-3-1-with-debian-stable/1197 => no luck, see error above

As you claim supporting 11 or higher I installed oracle java 12 as well (similar to https://tecadmin.net/install-oracle-java-11-ubuntu-18-04-bionic/) => see error above

Then I went back to good old java 8 (openjdk) using your install instructions for openjfx from http://help.jabref.org/en/Installation#jabref-4x-1

The version launches, however I get weird behavior using the search field in the top bar (the cursor does not move, when using the arrow keys) and I get the stacktrace appended at the end of the issue.

For now I switch back to the Jabref version from the Ubuntu packages by using sudo apt-get install jabref

Stacktrace:

File: grouptree.fxml not found, attempting with camel case
File: grouptree.css not found, attempting with camel case
java.lang.NullPointerException
	at com.sun.javafx.sg.prism.NGText.renderText(NGText.java:297)
	at com.sun.javafx.sg.prism.NGText.renderContent2D(NGText.java:270)
	at com.sun.javafx.sg.prism.NGShape.renderContent(NGShape.java:261)
	at com.sun.javafx.sg.prism.NGNode.doRender(NGNode.java:2053)
	at com.sun.javafx.sg.prism.NGNode.render(NGNode.java:1945)
	at com.sun.javafx.sg.prism.NGGroup.renderContent(NGGroup.java:235)
	at com.sun.javafx.sg.prism.NGRegion.renderContent(NGRegion.java:577)
	at com.sun.javafx.sg.prism.NGNode.renderForClip(NGNode.java:2294)
	at com.sun.javafx.sg.prism.NGNode.renderRectClip(NGNode.java:2188)
	at com.sun.javafx.sg.prism.NGNode.renderClip(NGNode.java:2214)
	at com.sun.javafx.sg.prism.NGNode.doRender(NGNode.java:2047)
	at com.sun.javafx.sg.prism.NGNode.render(NGNode.java:1945)
	at com.sun.javafx.sg.prism.NGGroup.renderContent(NGGroup.java:235)
	at com.sun.javafx.sg.prism.NGRegion.renderContent(NGRegion.java:577)
	at com.sun.javafx.sg.prism.NGNode.doRender(NGNode.java:2053)
	at com.sun.javafx.sg.prism.NGNode.render(NGNode.java:1945)
	at com.sun.javafx.tk.quantum.ViewPainter.doPaint(ViewPainter.java:477)
	at com.sun.javafx.tk.quantum.ViewPainter.paintImpl(ViewPainter.java:323)
	at com.sun.javafx.tk.quantum.UploadingPainter.run(UploadingPainter.java:134)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
	at com.sun.javafx.tk.RenderJob.run(RenderJob.java:58)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at com.sun.javafx.tk.quantum.QuantumRenderer$PipelineRunnable.run(QuantumRenderer.java:125)
	at java.lang.Thread.run(Thread.java:748)
10:21:32.777 [AWT-EventQueue-1] ERROR org.jabref.FallbackExceptionHandler - Uncaught exception occurred in Thread[AWT-EventQueue-1,6,main]
java.lang.NullPointerException: null
	at com.sun.javafx.text.PrismTextLayout.getCaretShape(PrismTextLayout.java:317) ~[jfxrt.jar:?]
	at javafx.scene.text.Text$TextAttribute$11.computeValue(Text.java:1787) ~[jfxrt.jar:?]
	at javafx.scene.text.Text$TextAttribute$11.computeValue(Text.java:1777) ~[jfxrt.jar:?]
	at javafx.beans.binding.ObjectBinding.get(ObjectBinding.java:153) ~[jfxrt.jar:?]
	at javafx.beans.binding.ObjectExpression.getValue(ObjectExpression.java:50) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase.get(ObjectPropertyBase.java:132) ~[jfxrt.jar:?]
	at com.sun.javafx.scene.control.skin.TextFieldSkin.lambda$new$4(TextFieldSkin.java:233) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:137) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase.fireValueChangedEvent(ObjectPropertyBase.java:105) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:112) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase.access$000(ObjectPropertyBase.java:51) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase$Listener.invalidated(ObjectPropertyBase.java:233) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:137) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) ~[jfxrt.jar:?]
	at javafx.beans.binding.ObjectBinding.invalidate(ObjectBinding.java:172) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.impl_geomChanged(Text.java:769) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.needsTextLayout(Text.java:194) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.needsFullTextLayout(Text.java:189) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.access$200(Text.java:95) ~[jfxrt.jar:?]
	at javafx.scene.text.Text$2.invalidated(Text.java:389) ~[jfxrt.jar:?]
	at javafx.beans.property.StringPropertyBase.markInvalid(StringPropertyBase.java:109) ~[jfxrt.jar:?]
	at javafx.beans.property.StringPropertyBase.access$000(StringPropertyBase.java:49) ~[jfxrt.jar:?]
	at javafx.beans.property.StringPropertyBase$Listener.invalidated(StringPropertyBase.java:230) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:137) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) ~[jfxrt.jar:?]
	at javafx.beans.binding.StringBinding.invalidate(StringBinding.java:171) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.BindingHelperObserver.invalidated(BindingHelperObserver.java:51) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:349) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) ~[jfxrt.jar:?]
	at javafx.scene.control.TextInputControl$TextProperty.fireValueChangedEvent(TextInputControl.java:1389) ~[jfxrt.jar:?]
	at javafx.scene.control.TextInputControl$TextProperty.markInvalid(TextInputControl.java:1393) ~[jfxrt.jar:?]
	at javafx.scene.control.TextInputControl$TextProperty.set(TextInputControl.java:1324) ~[jfxrt.jar:?]
	at javafx.scene.control.TextInputControl.setText(TextInputControl.java:349) ~[jfxrt.jar:?]
	at org.jabref.gui.search.GlobalSearchBar.clearSearch(GlobalSearchBar.java:328) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.search.GlobalSearchBar.performSearch(GlobalSearchBar.java:356) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.BasePanel$SearchListener.listen(BasePanel.java:2095) ~[JabRef-4.3.1.jar:?]
	at sun.reflect.GeneratedMethodAccessor14.invoke(Unknown Source) ~[?:?]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_222]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_222]
	at com.google.common.eventbus.Subscriber.invokeSubscriberMethod(Subscriber.java:87) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber$SynchronizedSubscriber.invokeSubscriberMethod(Subscriber.java:144) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber$1.run(Subscriber.java:72) ~[JabRef-4.3.1.jar:?]
	at com.google.common.util.concurrent.MoreExecutors$DirectExecutor.execute(MoreExecutors.java:398) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber.dispatchEvent(Subscriber.java:67) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Dispatcher$PerThreadQueuedDispatcher.dispatch(Dispatcher.java:108) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.EventBus.post(EventBus.java:212) ~[JabRef-4.3.1.jar:?]
	at org.jabref.model.database.BibDatabase.relayEntryChangeEvent(BibDatabase.java:582) ~[JabRef-4.3.1.jar:?]
	at sun.reflect.GeneratedMethodAccessor7.invoke(Unknown Source) ~[?:?]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_222]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_222]
	at com.google.common.eventbus.Subscriber.invokeSubscriberMethod(Subscriber.java:87) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber$SynchronizedSubscriber.invokeSubscriberMethod(Subscriber.java:144) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber$1.run(Subscriber.java:72) ~[JabRef-4.3.1.jar:?]
	at com.google.common.util.concurrent.MoreExecutors$DirectExecutor.execute(MoreExecutors.java:398) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber.dispatchEvent(Subscriber.java:67) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Dispatcher$PerThreadQueuedDispatcher.dispatch(Dispatcher.java:108) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.EventBus.post(EventBus.java:212) ~[JabRef-4.3.1.jar:?]
	at org.jabref.model.entry.BibEntry.clearField(BibEntry.java:483) ~[JabRef-4.3.1.jar:?]
	at org.jabref.model.entry.BibEntry.clearField(BibEntry.java:455) ~[JabRef-4.3.1.jar:?]
	at org.jabref.migrations.MergeReviewIntoCommentMigration.updateFields(MergeReviewIntoCommentMigration.java:73) ~[JabRef-4.3.1.jar:?]
	at org.jabref.migrations.MergeReviewIntoCommentMigration.migrate(MergeReviewIntoCommentMigration.java:66) ~[JabRef-4.3.1.jar:?]
	at org.jabref.migrations.MergeReviewIntoCommentMigration.lambda$performMigration$2(MergeReviewIntoCommentMigration.java:32) ~[JabRef-4.3.1.jar:?]
	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183) ~[?:1.8.0_222]
	at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) ~[?:1.8.0_222]
	at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) ~[?:1.8.0_222]
	at java.util.Iterator.forEachRemaining(Iterator.java:116) ~[?:1.8.0_222]
	at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) ~[?:1.8.0_222]
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482) ~[?:1.8.0_222]
	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472) ~[?:1.8.0_222]
	at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150) ~[?:1.8.0_222]
	at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173) ~[?:1.8.0_222]
	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) ~[?:1.8.0_222]
	at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485) ~[?:1.8.0_222]
	at org.jabref.migrations.MergeReviewIntoCommentMigration.performMigration(MergeReviewIntoCommentMigration.java:32) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.importer.actions.MergeReviewIntoCommentAction.performAction(MergeReviewIntoCommentAction.java:21) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.importer.actions.OpenDatabaseAction.performPostOpenActions(OpenDatabaseAction.java:93) ~[JabRef-4.3.1.jar:?]
	at org.jabref.JabRefGUI.openWindow(JabRefGUI.java:186) ~[JabRef-4.3.1.jar:?]
	at org.jabref.JabRefGUI.<init>(JabRefGUI.java:67) ~[JabRef-4.3.1.jar:?]
	at org.jabref.JabRefMain.lambda$start$1(JabRefMain.java:128) ~[JabRef-4.3.1.jar:?]
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) [?:1.8.0_222]
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) [?:1.8.0_222]
	at java.awt.EventQueue.access$500(EventQueue.java:97) [?:1.8.0_222]
	at java.awt.EventQueue$3.run(EventQueue.java:709) [?:1.8.0_222]
	at java.awt.EventQueue$3.run(EventQueue.java:703) [?:1.8.0_222]
	at java.security.AccessController.doPrivileged(Native Method) [?:1.8.0_222]
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) [?:1.8.0_222]
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) [?:1.8.0_222]
	at org.GNOME.Accessibility.AtkWrapper$6.dispatchEvent(AtkWrapper.java:715) [java-atk-wrapper.jar:?]
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) [?:1.8.0_222]
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [?:1.8.0_222]
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [?:1.8.0_222]
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [?:1.8.0_222]
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [?:1.8.0_222]
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [?:1.8.0_222]




Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions