jabref not starting on Linux #7105

sambo57u · 2020-11-16T15:47:26Z

JabRef 5.2--2020-11-16--1dc91ca
Installed from rpm
Fedora Linux 33

After updating to the devel version of today the jabref fails to start with error message:

Error: Could not find or load main class org.jabref/org.jabref.gui.JabRefLauncher in module org.jabref

this is by executing /opt/jabref/bin/JabRef OR the script in /opt/jabref/lib/runtime/bin

Changing the srcript line to:
"$DIR/java" -p "$DIR/../../app" -m org.jabref/org.jabref.gui.JabRefLauncher "$@"
works.

juejung · 2020-11-16T18:27:59Z

Same problem with .deb version https://builds.jabref.org/master/jabref_5.2-1_amd64.deb from 11/16/20 on Ubuntu 18.04.
Haven't tried changing the script line as suggested above.

Siedlerchr · 2020-11-16T19:08:48Z

Hmm I did some changes yesterday, maybe need to revert some back. The script is normally auto-generated.

ilippert · 2020-11-17T06:35:27Z

Same here - does not start jabref-5.2.255-1.x86_64

ilippert · 2020-11-17T06:40:13Z

Changing the srcript line to:
"$DIR/java" -p "$DIR/../../app" -m org.jabref/org.jabref.gui.JabRefLauncher "$@"
works.

Maybe I misunderstood - I edited /opt/jabref/lib/runtime/bin/JabRefwith the suggested line. Still does not run.
Fedora 33.

Siedlerchr · 2020-11-17T08:28:39Z

Can you please test the version from here? I reverted some changes, so hopeuflly it works again:
https://builds.jabref.org/pull/7107/merge/

AtrusRiven · 2020-11-17T11:55:22Z

On Windows neither (no reaction at all). Neither with the actual master nor with the 7107 @Siedlerchr mentioned.

juejung · 2020-11-17T14:02:09Z

Just tried https://builds.jabref.org/pull/7107/merge/
It still does not start. Tested on Ubuntu 20.04
I had to revert to the version from last Thursday (.deb package from 11/12/2020)

sambo57u · 2020-11-17T14:27:55Z

Same here using the rpm version on Fedora 33. Here is one hint, the automatically generated script contains the line:

"$DIR/java" -p "$DIR/../app" -m org.jabref/org.jabref/org.jabref.gui.JabRefLauncher "$@"

note the repeated org.jabref after -m. Replacing this with:

"$DIR/java" -p "$DIR/../app" -m org.jabref/org.jabref.gui.JabRefLauncher "$@"

works!

Siedlerchr · 2020-11-17T15:31:57Z

@sambo57u Thanks for the hint!
Can you please all try with the new version from here? https://builds.jabref.org/pull/7107/merge/ That should be correct again

juejung · 2020-11-17T16:05:20Z

Ok, the .deb version from https://builds.jabref.org/pull/7107/merge/ works again on Ubuntu 20.04. Thanks.

sambo57u · 2020-11-17T16:25:44Z

It is also working (rpm version) on Fedora 33.

AtrusRiven · 2020-11-17T16:28:30Z

Working for Win10, too. Thanks a lot!

Siedlerchr · 2020-11-17T16:38:28Z

Thanks for the quick feedback! I merged the fix now (currently building) , so all master versions will then work again.
The culprit was a gradle update that required modifications withthe nodulebname

ilippert · 2020-11-17T23:18:46Z

solved

JabRef 5.2--2020-11-17--a335f0d
Linux 5.9.8-200.fc33.x86_64 amd64
Java 15.0.1

mlep · 2020-11-18T09:05:21Z

@ilippert With this version, and under Linux, JabRef opens but the "group" and the "web search" interfaces do not open. An exception is raised.
Do you have the same issue?

Exception details:
java.lang.IllegalStateException: Cannot load org.jabref.gui.groups.grouptree
at [email protected]/com.airhacks.afterburner.views.ViewLoader.load(Unknown Source)
at [email protected]/org.jabref.gui.groups.GroupSidePane.createContentPane(Unknown Source)
at [email protected]/org.jabref.gui.SidePaneComponent.getContentPane(Unknown Source)
at [email protected]/org.jabref.gui.SidePane.setComponents(Unknown Source)
at [email protected]/org.jabref.gui.SidePaneManager.updateView(Unknown Source)
at [email protected]/org.jabref.gui.SidePaneManager.show(Unknown Source)
at [email protected]/org.jabref.gui.SidePaneManager.toggle(Unknown Source)
at [email protected]/org.jabref.gui.SidePaneComponent$ToggleCommand.execute(Unknown Source)
at [email protected]/org.jabref.gui.actions.JabRefAction.lambda$new$3(Unknown Source)
at [email protected]/org.controlsfx.control.action.Action.handle(Unknown Source)
at [email protected]/org.controlsfx.control.action.Action.handle(Unknown Source)
at [email protected]/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
at [email protected]/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
at [email protected]/javafx.event.Event.fireEvent(Unknown Source)
at [email protected]/javafx.scene.control.MenuItem.fire(Unknown Source)
at [email protected]/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(Unknown Source)
at [email protected]/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(Unknown Source)
at [email protected]/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
at [email protected]/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
at [email protected]/javafx.event.Event.fireEvent(Unknown Source)
at [email protected]/javafx.scene.Scene$MouseHandler.process(Unknown Source)
at [email protected]/javafx.scene.Scene.processMouseEvent(Unknown Source)
at [email protected]/javafx.scene.Scene$ScenePeerListener.mouseEvent(Unknown Source)
at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
at java.base/java.security.AccessController.doPrivileged(Unknown Source)
at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(Unknown Source)
at [email protected]/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)
at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(Unknown Source)
at [email protected]/com.sun.glass.ui.View.handleMouseEvent(Unknown Source)
at [email protected]/com.sun.glass.ui.View.notifyMouse(Unknown Source)
at [email protected]/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
at [email protected]/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: javafx.fxml.LoadException:
/org.jabref/org/jabref/gui/groups/GroupTree.fxml

at [email protected]/javafx.fxml.FXMLLoader.constructLoadException(Unknown Source)
at [email protected]/javafx.fxml.FXMLLoader.loadImpl(Unknown Source)
at [email protected]/javafx.fxml.FXMLLoader.loadImpl(Unknown Source)
at [email protected]/javafx.fxml.FXMLLoader.load(Unknown Source)
... 52 more

Caused by: java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.javafx.reflect.Trampoline.invoke(Unknown Source)
at jdk.internal.reflect.GeneratedMethodAccessor5.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at [email protected]/com.sun.javafx.reflect.MethodUtil.invoke(Unknown Source)
at [email protected]/com.sun.javafx.fxml.MethodHelper.invoke(Unknown Source)
... 55 more
Caused by: java.lang.NullPointerException: Cannot invoke "javafx.scene.control.TreeItem.getValue()" because "" is null
at [email protected]/org.jabref.gui.groups.GroupTreeView.getTreeItemByValue(Unknown Source)
at [email protected]/org.jabref.gui.groups.GroupTreeView.getTreeItemByValue(Unknown Source)
at [email protected]/org.jabref.gui.groups.GroupTreeView.selectNode(Unknown Source)
at [email protected]/org.jabref.gui.groups.GroupTreeView.selectNode(Unknown Source)
at java.base/java.lang.Iterable.forEach(Unknown Source)
at [email protected]/org.jabref.gui.groups.GroupTreeView.lambda$initialize$0(Unknown Source)
at [email protected]/org.jabref.gui.util.BindingsHelper.bindContentBidirectional(Unknown Source)
at [email protected]/org.jabref.gui.util.BindingsHelper.bindContentBidirectional(Unknown Source)
at [email protected]/org.jabref.gui.groups.GroupTreeView.initialize(Unknown Source)
... 65 more

Siedlerchr · 2020-11-18T09:10:59Z

@mlep The group error is probably related to another issue which was fixed recently

mlep · 2020-11-18T09:15:56Z

@Siedlerchr OK, thanks for the info. I will wait for the next build.

ilippert · 2020-11-18T09:19:47Z

@ilippert With this version, and under Linux, JabRef opens but the "group" and the "web search" interfaces do not open. An exception is raised.
Do you have the same issue?

at
JabRef 5.2--2020-11-17--a335f0d
Linux 5.9.8-200.fc33.x86_64 amd64
Java 15.0.1
I cannot use the Google Search; but I can use the groups.

mlep · 2020-11-18T12:33:42Z

In JabRef 5.2--2020-11-18--6669a6e too, The group window does not open and an exception is raised.
@Siedlerchr: please, could you point me to the relevant issue?

Siedlerchr · 2020-11-18T12:43:25Z

@mlep #6999 and #7096 was the fix. Guess it may have something to do with the group color stuff

mlep · 2020-11-19T11:00:06Z

@Siedlerchr Does it require a new issue to be created?

Siedlerchr · 2020-11-21T16:56:51Z

@mlep Does it work again in the latest master?

sambo57u · 2020-11-21T17:08:02Z

Yes, it is working on the current master jabref-5.2.272

mlep · 2020-11-21T19:35:06Z

@Siedlerchr I still have the issue with the group panel with the version
JabRef 5.2--2020-11-21--6f35c36
Linux 4.19.0-12-amd64 amd64
Java 15.0.1

Some details:
With the group panel initially closed,

if no file is opened on startup, the group panel opens and closes fine.
if a file (like https://github.com/JabRef/jabref/blob/master/src/test/resources/testbib/jabref-authors.bib) is already opened at startup, opening the group panel raises an exception:

Uncaught exception occurred in Thread[JavaFx Application Thread,5,main]
Cannot load org.jabref.gui.groups.grouptree
java.lang.IllegalStateException: Cannot load org.jabref.gui.groups.grouptree
at [email protected]/com.airhacks.afterburner.views.ViewLoader.load(Unknown Source)
at [email protected]/org.jabref.gui.groups.GroupSidePane.createContentPane(Unknown Source)
at [email protected]/org.jabref.gui.SidePaneComponent.getContentPane(Unknown Source)
at [email protected]/org.jabref.gui.SidePane.setComponents(Unknown Source)
at [email protected]/org.jabref.gui.SidePaneManager.updateView(Unknown Source)
at [email protected]/org.jabref.gui.SidePaneManager.show(Unknown Source)
at [email protected]/org.jabref.gui.SidePaneManager.toggle(Unknown Source)
at [email protected]/org.jabref.gui.SidePaneComponent$ToggleCommand.execute(Unknown Source)
at [email protected]/org.jabref.gui.actions.JabRefAction.lambda$new$3(Unknown Source)
at [email protected]/org.controlsfx.control.action.Action.handle(Unknown Source)
at [email protected]/org.controlsfx.control.action.Action.handle(Unknown Source)
at [email protected]/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
at [email protected]/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
at [email protected]/javafx.event.Event.fireEvent(Unknown Source)
at [email protected]/javafx.scene.control.MenuItem.fire(Unknown Source)
at [email protected]/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(Unknown Source)
at [email protected]/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(Unknown Source)
at [email protected]/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at [email protected]/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
at [email protected]/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
at [email protected]/javafx.event.Event.fireEvent(Unknown Source)
at [email protected]/javafx.scene.Scene$MouseHandler.process(Unknown Source)
at [email protected]/javafx.scene.Scene.processMouseEvent(Unknown Source)
at [email protected]/javafx.scene.Scene$ScenePeerListener.mouseEvent(Unknown Source)
at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
at java.base/java.security.AccessController.doPrivileged(Unknown Source)
at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(Unknown Source)
at [email protected]/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)
at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(Unknown Source)
at [email protected]/com.sun.glass.ui.View.handleMouseEvent(Unknown Source)
at [email protected]/com.sun.glass.ui.View.notifyMouse(Unknown Source)
at [email protected]/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
at [email protected]/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: javafx.fxml.LoadException:
/org.jabref/org/jabref/gui/groups/GroupTree.fxml

at [email protected]/javafx.fxml.FXMLLoader.constructLoadException(Unknown Source)
at [email protected]/javafx.fxml.FXMLLoader.loadImpl(Unknown Source)
at [email protected]/javafx.fxml.FXMLLoader.loadImpl(Unknown Source)
at [email protected]/javafx.fxml.FXMLLoader.load(Unknown Source)
... 52 more

Caused by: java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.javafx.reflect.Trampoline.invoke(Unknown Source)
at jdk.internal.reflect.GeneratedMethodAccessor6.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at [email protected]/com.sun.javafx.reflect.MethodUtil.invoke(Unknown Source)
at [email protected]/com.sun.javafx.fxml.MethodHelper.invoke(Unknown Source)
... 55 more
Caused by: java.lang.NullPointerException: Cannot invoke "javafx.scene.control.TreeItem.getValue()" because "" is null
at [email protected]/org.jabref.gui.groups.GroupTreeView.getTreeItemByValue(Unknown Source)
at [email protected]/org.jabref.gui.groups.GroupTreeView.getTreeItemByValue(Unknown Source)
at [email protected]/org.jabref.gui.groups.GroupTreeView.selectNode(Unknown Source)
at [email protected]/org.jabref.gui.groups.GroupTreeView.selectNode(Unknown Source)
at java.base/java.lang.Iterable.forEach(Unknown Source)
at [email protected]/org.jabref.gui.groups.GroupTreeView.lambda$initialize$0(Unknown Source)
at [email protected]/org.jabref.gui.util.BindingsHelper.bindContentBidirectional(Unknown Source)
at [email protected]/org.jabref.gui.util.BindingsHelper.bindContentBidirectional(Unknown Source)
at [email protected]/org.jabref.gui.groups.GroupTreeView.initialize(Unknown Source)
... 65 more

Siedlerchr added the os: linux label Nov 16, 2020

Siedlerchr added the build-system label Nov 17, 2020

Siedlerchr mentioned this issue Nov 17, 2020

Installation problem with 5.2.257-1 (17 Nov 2020) #7109

Closed

1 task

Siedlerchr closed this as completed Nov 18, 2020

Siedlerchr mentioned this issue Nov 21, 2020

NPE in groups panel opening #7114

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jabref not starting on Linux #7105

jabref not starting on Linux #7105

sambo57u commented Nov 16, 2020

juejung commented Nov 16, 2020 •

edited

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Siedlerchr commented Nov 16, 2020 •

edited

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ilippert commented Nov 17, 2020

ilippert commented Nov 17, 2020 •

edited

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Siedlerchr commented Nov 17, 2020

AtrusRiven commented Nov 17, 2020

juejung commented Nov 17, 2020

sambo57u commented Nov 17, 2020

Siedlerchr commented Nov 17, 2020

juejung commented Nov 17, 2020

sambo57u commented Nov 17, 2020

AtrusRiven commented Nov 17, 2020

Siedlerchr commented Nov 17, 2020

ilippert commented Nov 17, 2020 •

edited

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mlep commented Nov 18, 2020

Siedlerchr commented Nov 18, 2020

mlep commented Nov 18, 2020

ilippert commented Nov 18, 2020

mlep commented Nov 18, 2020

Siedlerchr commented Nov 18, 2020

mlep commented Nov 19, 2020

Siedlerchr commented Nov 21, 2020

sambo57u commented Nov 21, 2020

mlep commented Nov 21, 2020

jabref not starting on Linux #7105

jabref not starting on Linux #7105

Comments

sambo57u commented Nov 16, 2020

juejung commented Nov 16, 2020 • edited Loading

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ilippert commented Nov 17, 2020

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