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 org.jabref@5.14.60000/org.jabref.logic.journals.AbbreviationParser.detectDelimiter(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.logic.journals.AbbreviationParser.readJournalListFromFile(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.logic.journals.JournalAbbreviationLoader.readAbbreviationsFromCsvFile(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.logic.journals.JournalAbbreviationLoader.loadRepository(Unknown Source)
	at org.jabref@5.14.60000/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 javafx.graphics@22.0.1/com.sun.javafx.application.LauncherImpl.launchApplication1(Unknown Source)
	at javafx.graphics@22.0.1/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 org.jabref@5.14.60000/org.jabref.gui.maintable.SmartConstrainedResizePolicy.getContentWidth(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.maintable.SmartConstrainedResizePolicy.initColumnSize(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.maintable.SmartConstrainedResizePolicy.call(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.maintable.SmartConstrainedResizePolicy.call(Unknown Source)
	at javafx.controls@22.0.1/javafx.scene.control.TableView$6.invalidated(Unknown Source)
	at javafx.base@22.0.1/javafx.beans.property.ObjectPropertyBase.markInvalid(Unknown Source)
	at javafx.base@22.0.1/javafx.beans.property.ObjectPropertyBase.set(Unknown Source)
	at javafx.controls@22.0.1/javafx.scene.control.TableView.setColumnResizePolicy(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.maintable.MainTable.<init>(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.LibraryTab.createMainTable(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.LibraryTab.setupMainPanel(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.LibraryTab.<init>(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.LibraryTab.createLibraryTab(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.importer.actions.OpenDatabaseAction.openTheFile(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.importer.actions.OpenDatabaseAction.lambda$openFiles$0(Unknown Source)
	at java.base/java.lang.Iterable.forEach(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.importer.actions.OpenDatabaseAction.openFiles(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.frame.JabRefFrame.openLastEditedDatabases(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.JabRefGUI.onShowing(Unknown Source)
	at javafx.base@22.0.1/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
	at javafx.base@22.0.1/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at javafx.base@22.0.1/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at javafx.base@22.0.1/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
	at javafx.base@22.0.1/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at javafx.base@22.0.1/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at javafx.base@22.0.1/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
	at javafx.base@22.0.1/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
	at javafx.base@22.0.1/javafx.event.Event.fireEvent(Unknown Source)
	at javafx.graphics@22.0.1/javafx.stage.Window.fireEvent(Unknown Source)
	at javafx.graphics@22.0.1/javafx.stage.Window$12.invalidated(Unknown Source)
	at javafx.base@22.0.1/javafx.beans.property.BooleanPropertyBase.markInvalid(Unknown Source)
	at javafx.base@22.0.1/javafx.beans.property.BooleanPropertyBase.set(Unknown Source)
	at javafx.graphics@22.0.1/javafx.stage.Window.setShowing(Unknown Source)
	at javafx.graphics@22.0.1/javafx.stage.Window.show(Unknown Source)
	at javafx.graphics@22.0.1/javafx.stage.Stage.show(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.JabRefGUI.openWindow(Unknown Source)
	at org.jabref@5.14.60000/org.jabref.gui.JabRefGUI.start(Unknown Source)
	at javafx.graphics@22.0.1/com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(Unknown Source)
	at javafx.graphics@22.0.1/com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(Unknown Source)
	at javafx.graphics@22.0.1/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source)
	at java.base/java.security.AccessController.doPrivileged(Unknown Source)
	at javafx.graphics@22.0.1/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source)
	at javafx.graphics@22.0.1/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
	at javafx.graphics@22.0.1/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
	at javafx.graphics@22.0.1/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")