jabref snap fails to start on ubuntu

[RJDan]

JabRef version

5.14 (latest release)

Operating system

GNU / Linux

Details on version and operating system

OS: Ubuntu 24.04 LTS x86_64 Host: OptiPlex 7050 Kernel: 6.8.0-36-generic Uptime: 1 hour, 49 mins Packages: 2397 (dpkg), 6 (flatpak), 79 (snap) Shell: bash 5.2.21 Resolution: 2560x1440 WM: sway Terminal: kitty CPU: Intel i5-7600 (4) @ 4.100GHz GPU: Intel HD Graphics 630 GPU: AMD ATI Radeon HD 8830M / R7 250 / R7 M465X Memory: 9739MiB / 31960MiB

Checked with the latest development build (copy version output from About dialog)

• I made a backup of my libraries before testing the latest development version.
• I have tested the latest development version and the problem persists

Steps to reproduce the behaviour

1. Start Jabref from terminal or launcher (fuzzel)
2. Nothing happens.

commands:
  - jabref.browser-proxy
  - jabref
snap-id:      T5x6neyM0Uc9OWDHGorm61NKxh3Bd47k
tracking:     latest/stable
refresh-date: today at 10:32 CEST
channels:
  latest/stable:    5.14.60000 2024-07-08 (3221) 217MB -
  latest/candidate: 5.14.60000 2024-07-08 (3221) 217MB -
  latest/beta:      5.14.60000 2024-07-08 (3221) 217MB -
  latest/edge:      5.14.60000 2024-07-08 (3221) 217MB -
installed:          5.14.60000            (3221) 217MB -

Appendix

This is what was printed to screen when I start the snap from the terminal.

Picked up _JAVA_OPTIONS: -Duser.home=/home/rjd/snap/jabref/3221
Messages are not initialized before accessing key: Display help on command line options
2024-07-09 12:07:23 [main] org.jabref.logic.journals.JournalAbbreviationLoader.loadRepository()
ERROR: Cannot read external journal list file /home/rjd/JabRef/abbrv.jabref.org/journalList_dots.csv: java.nio.file.NoSuchFileException: /home/rjd/JabRef/abbrv.jabref.org/journalList_dots.csv
	at java.base/sun.nio.fs.UnixException.translateToIOException(Unknown Source)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown Source)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown Source)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(Unknown Source)
	at java.base/java.nio.file.Files.newByteChannel(Unknown Source)
	at java.base/java.nio.file.Files.newByteChannel(Unknown Source)
	at java.base/java.nio.file.spi.FileSystemProvider.newInputStream(Unknown Source)
	at java.base/java.nio.file.Files.newInputStream(Unknown Source)
	at java.base/java.nio.file.Files.newBufferedReader(Unknown Source)
	at [email protected]/org.jabref.logic.journals.AbbreviationParser.detectDelimiter(Unknown Source)
	at [email protected]/org.jabref.logic.journals.AbbreviationParser.readJournalListFromFile(Unknown Source)
	at [email protected]/org.jabref.logic.journals.JournalAbbreviationLoader.readAbbreviationsFromCsvFile(Unknown Source)
	at [email protected]/org.jabref.logic.journals.JournalAbbreviationLoader.loadRepository(Unknown Source)
	at [email protected]/org.jabref.Launcher.main(Unknown Source)
Gtk-Message: 12:07:24.201: Not loading module "atk-bridge": The functionality is provided by GTK natively. Please try to not load it.
2024-07-09 12:07:24 [JavaFX Application Thread] org.jabref.gui.theme.ThemeManager.updateThemeSettings()
INFO: Not updating theme because it hasn't changed
2024-07-09 12:07:24 [JavaFX Application Thread] org.jabref.gui.theme.ThemeManager.updateThemeSettings()
INFO: Theme set to Theme{type=CUSTOM, name='/home/rjd/msRNA_Mobile/JabRef/JabRef_themes/customDarkTheme_220128.css'} with base css StyleSheet{jrt:/org.jabref/org/jabref/gui/Base.css}
2024-07-09 12:07:24 [JavaFX Application Thread] org.jabref.gui.theme.ThemeManager.addStylesheetToWatchlist()
INFO: Watching css /home/rjd/msRNA_Mobile/JabRef/JabRef_themes/customDarkTheme_220128.css for live updates
2024-07-09 12:07:25 [JavaFX Application Thread] org.jabref.gui.StateManager.setActiveDatabase()
INFO: No open database detected
Exception in Application start method
2024-07-09 12:07:27 [main] org.jabref.Launcher.main()
ERROR: Unexpected exception: java.lang.RuntimeException: Exception in Application start method
	at [email protected]/com.sun.javafx.application.LauncherImpl.launchApplication1(Unknown Source)
	at [email protected]/com.sun.javafx.application.LauncherImpl.lambda$launchApplication$2(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private double javafx.scene.control.TableView.contentWidth accessible: module javafx.controls does not "opens javafx.scene.control" to module org.jabref
	at java.base/java.lang.reflect.AccessibleObject.throwInaccessibleObjectException(Unknown Source)
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(Unknown Source)
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(Unknown Source)
	at java.base/java.lang.reflect.Field.checkCanSetAccessible(Unknown Source)
	at java.base/java.lang.reflect.Field.setAccessible(Unknown Source)
	at [email protected]/org.jabref.gui.maintable.SmartConstrainedResizePolicy.getContentWidth(Unknown Source)
	at [email protected]/org.jabref.gui.maintable.SmartConstrainedResizePolicy.initColumnSize(Unknown Source)
	at [email protected]/org.jabref.gui.maintable.SmartConstrainedResizePolicy.call(Unknown Source)
	at [email protected]/org.jabref.gui.maintable.SmartConstrainedResizePolicy.call(Unknown Source)
	at [email protected]/javafx.scene.control.TableView$6.invalidated(Unknown Source)
	at [email protected]/javafx.beans.property.ObjectPropertyBase.markInvalid(Unknown Source)
	at [email protected]/javafx.beans.property.ObjectPropertyBase.set(Unknown Source)
	at [email protected]/javafx.scene.control.TableView.setColumnResizePolicy(Unknown Source)
	at [email protected]/org.jabref.gui.maintable.MainTable.<init>(Unknown Source)
	at [email protected]/org.jabref.gui.LibraryTab.createMainTable(Unknown Source)
	at [email protected]/org.jabref.gui.LibraryTab.setupMainPanel(Unknown Source)
	at [email protected]/org.jabref.gui.LibraryTab.<init>(Unknown Source)
	at [email protected]/org.jabref.gui.LibraryTab.createLibraryTab(Unknown Source)
	at [email protected]/org.jabref.gui.importer.actions.OpenDatabaseAction.openTheFile(Unknown Source)
	at [email protected]/org.jabref.gui.importer.actions.OpenDatabaseAction.lambda$openFiles$0(Unknown Source)
	at java.base/java.lang.Iterable.forEach(Unknown Source)
	at [email protected]/org.jabref.gui.importer.actions.OpenDatabaseAction.openFiles(Unknown Source)
	at [email protected]/org.jabref.gui.frame.JabRefFrame.openLastEditedDatabases(Unknown Source)
	at [email protected]/org.jabref.gui.JabRefGUI.onShowing(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.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.stage.Window.fireEvent(Unknown Source)
	at [email protected]/javafx.stage.Window$12.invalidated(Unknown Source)
	at [email protected]/javafx.beans.property.BooleanPropertyBase.markInvalid(Unknown Source)
	at [email protected]/javafx.beans.property.BooleanPropertyBase.set(Unknown Source)
	at [email protected]/javafx.stage.Window.setShowing(Unknown Source)
	at [email protected]/javafx.stage.Window.show(Unknown Source)
	at [email protected]/javafx.stage.Stage.show(Unknown Source)
	at [email protected]/org.jabref.gui.JabRefGUI.openWindow(Unknown Source)
	at [email protected]/org.jabref.gui.JabRefGUI.start(Unknown Source)
	at [email protected]/com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(Unknown Source)
	at [email protected]/com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(Unknown Source)
	at [email protected]/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source)
	at java.base/java.security.AccessController.doPrivileged(Unknown Source)
	at [email protected]/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source)
	at [email protected]/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(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$10(Unknown Source)
	... 1 more

[calixtus]

I don't get it, how have we missed this? We tested the build and the installer... Hot fix will be done tonight.

[RJDan]

Thanks for the quick response!!

[koppor]

Background: The snap-distributed version is a wrapper around the portable linux version of https://builds.jabref.org/main/ (in a state in a a certain point of time in the past)

---

I checked the current portable file. And it does not contain any journals. Need to investiage. (Also indicated by the output ERROR: Cannot read external journal list file /home/rjd/JabRef/abbrv.jabref.org/journalList_dots.csv above)

Update: The word "external" is important here. Seems like there is some local configuration and path mapping issues. Not release-criticial IMHO - and another issue.

Update One needs to open JabRef-100.0.jar. There, one finds journals/journal-list.mv. No need to worry.

[koppor]

Unable to make field private double javafx.scene.control.TableView.contentWidth accessible: module javafx.controls does not "opens javafx.scene.control" to module org.jabref

But we have in our build.gradle following lines:

jabref/build.gradle

Line 87 in 1505137

'--add-opens=javafx.controls/javafx.scene.control=org.jabref',

and

jabref/build.gradle

Line 492 in 1505137

'javafx.controls/javafx.scene.control' : 'org.jabref',

[Siedlerchr]

It would be interesting to see what is inside the cfg file inside the snap

[Siedlerchr]

I could reproduce this unter Ubuntu 22.04 LTS in a VM.

[Siedlerchr]

I found a workaround:
Go to /snap/jabref/3221/lib/runtime and run JabRef as program (right cllick "Run as program")

[calixtus]

Interestingly, works in Arch Linux

[Siedlerchr]

The problem is now fixed, you can use jabref from the --edge channel until we do a new release tomorrow

[OlafKleinBerlin]

I had a similar problem at Kubuntu 22.04 after the automatic update from 5.13 to 5.14. I managed to start jabref 5.14 by removing and reinstalling the package with snap. After loading a saved preference file from jabref 5.13 into jabref 5.14, I could no longer start jabref 5.14 until removing and reinstalling the package.

[koppor]

I had a similar problem at Kubuntu 22.04 after the automatic update from 5.13 to 5.14. I managed to start jabref 5.14 by removing and reinstalling the package with snap. After loading a saved preference file from jabref 5.13 into jabref 5.14, I could no longer start jabref 5.14 until removing and reinstalling the package.

@OlafKleinBerlin Could you share the preference file? Maybe also share what you changed in the preferences (not that important... An import should work...) It is really strange that this does not work...

[OlafKleinBerlin]

Dear koppor,

the preference file can be found in this post of me in the jabref forum.
When I was simply using jabref 5.14 without applying the workarounds discussed above, loading this preference file created an error message and afterwards I was not able to start JabRef without removing and reinstalling the package.

Later, I loaded this file using the workarounds discussed above and in the forum topic.
I got the error message discussed in my mentioned forum post, but I could start JabRef afterwards and it seemed that my preferences were applied. And according to this forum contribution an error for dealing with this file has been fixed.

[RJDan]

I upgraded to 5.15 and I can now launch Jabref! Thank you!

[calixtus]

Sorry for the inconvenience. Although we tested the app before releasing it, we did not run into this issue first. Thanks for your bug report and your patience.