JavaFX warnings

Do these warnings mean that JavaFX is not installed/configured correctly for JabRef?

Messages are not initialized before accessing key: Display help on command line options
2024-05-14 20:06:42 [JavaFX-Launcher] sun.util.logging.internal.LoggingProviderImpl$JULWrapper.log()
WARN: Unsupported JavaFX configuration: classes were loaded from 'module org.jabref.merged.module', isAutomatic: false, isOpen: true
2024-05-14 20:06:45 [JavaFX Application Thread] org.jabref.preferences.JabRefPreferences.getFetcherKeysFromKeyring()
WARN: JabRef could not open the key store

I am investigating this for two reasons:

  1. If something is wrong with my JabRef installation I want to fix it. In particular, startup has been very slow (black window for ~10s) and performance has really been lagging (I have already followed instructions on this. Right now I am only asking if JavaFX is working as it should).
  2. To demystify basic installation/usage of JavaFX as a JabRef user

JabRef info

JabRef 5.13--2024-04-01--6bdcf63
Linux 6.8.8-1-default amd64
Java 21.0.2 
JavaFX 22+30

System info

  • Operating system: openSUSE Tumbleweed.
  • OpenJDK: installed from the Tumbleweed repository.
  • OpenJFX: installed from the Tumbleweed repository.
  • JavaFX: SDK and jmods from gluonhq.



Note: PATH_TO_FX points to the Tumbleweed version. The SDK from Gluon is present in /opt/ but not added to PATH_TO_FX (I removed it to simplify troubleshooting/experimenting).

All the javafx.something modules required in jabref/src/main/java/ are present on my system in the paths above. I understand that they are also installed by JabRef in any case, but I do not know in which directory.

The output of java --list-modules does not show any javafx modules. Should they appear in this list?

Regarding the unsupported configuration warning, I have read these related/similar issues. I am posting these here to revisit myself and for the benefit of anyone else who might be fumbling around with java commands in the terminal:

Edit: the key store warning appears to be a bug (to be verified). I submitted a report on Github.

Picked up _JAVA_OPTIONS: --module-path=/usr/share/java/openjfx --add-modules=ALL-MODULE-PATH
Error occurred during initialization of boot layer
java.lang.module.FindException: Unable to derive module descriptor for /usr/share/java/openjfx/
Caused by: java.lang.module.InvalidModuleDescriptorException: CompileExternal.class found in top-level directory (unnamed package not allowed in module)
  • Why --add-module if already on the path (Stack Overflow).
    How to add modules or put them on the upgrade path. Any variations I try to add jmods to the list produces are error and fails. I don’t know if this is even necessary, but like I said, I am trying to demystify JavaFX since this has caused confusion on several occasions when I have installed JabRef on Windows or in WSL2.

If I remember right, this particular error has to do with your API keys and I believe it also emerges, if the number of API keys that are stored is zero. Do you have some API keys? Otherwise you can ignore it.

This is a false positive, kind of because not all third-party libraries used by JabRef are compatible with the java module system we use a plugin that merges them together into a single merged module together with JabRef code
And as some of them require javafx as well it is included in that as well

I have a key for Medline, which I am pretty sure was stored in JabRef previously but I can no longer see. Maybe this changed when I upgraded from 5.12 to 5.13 and I only noticed now, or maybe it has something to do with this: (Convert the "Custom API key" list to a table [#10926] by AbdAlRahmanGad · Pull Request #10936 · JabRef/jabref · GitHub). In any case, I have no keys now and cannot add any, so I reported this: Credential store is not supported · Issue #11296 · JabRef/jabref · GitHub

Thanks! This is what I suspected, because I had similar warnings in the past coupled with errors and malfunction when libraries were actually missing.