jabref won't run in Ubuntu 18.10

[pauljohn32]

On askubuntu.com, user asks about jabref error. On 18.10, jabref wont' start due to missing java modules. I answered that java 8 is required: https://askubuntu.com/a/1085678/495717. When java 11 is installed at same time, jabref won't start.

In my checking, one must actually remove java 11. I tried setting the preferred java version with "sudo update-alternatives --config java" is not sufficient, one must actually delete the newer java packages in order for jabref to start. If I set the preferred version, then jabref never appears on screen.

$ jabref
21:22:40.859 [AWT-EventQueue-0] ERROR net.sf.jabref.FallbackExceptionHandler - Uncaught exception Occurred in Thread[AWT-EventQueue-0,6,main]
java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
 at net.sf.jabref.logic.importer.ImportFormatReader.resetImportFormats(ImportFormatReader.java:56) ~[JabRef-3.8.2.jar:?]
 at net.sf.jabref.JabRefMain.start(JabRefMain.java:78) ~[JabRef-3.8.2.jar:?]
 at net.sf.jabref.JabRefMain.lambda$main$0(JabRefMain.java:40) ~[JabRef-3.8.2.jar:?]
 at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313) ~[?:?]
 at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770) ~[?:?]
 at java.awt.EventQueue$4.run(EventQueue.java:721) ~[?:?]
 at java.awt.EventQueue$4.run(EventQueue.java:715) ~[?:?]
 at java.security.AccessController.doPrivileged(Native Method) ~[?:?]
 at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) ~[?:?]
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:740) ~[?:?]
 at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) [?:?]
 at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) [?:?]
 at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) [?:?]
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) [?:?]
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [?:?]
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:90) [?:?]
Caused by: java.lang.ClassNotFoundException: javax.xml.bind.JAXBException
 at jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582) ~[?:?]
 at jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178) ~[?:?]
 at java.lang.ClassLoader.loadClass(ClassLoader.java:521) ~[?:?]
 ... 16 more

I've downloaded the newest Jabref package, can't launch it either if java 11 is installed.

$ java -jar JabRef-4.3.1.jar
Error: Could not find or load main class org.jabref.JabRefMain

I wonder if the version of java could be specified differently in the Ubuntu wrapping to solve this.

[Launchpad Janitor (janitor)]

Status changed to 'Confirmed' because the bug affects multiple users.

[gregor herrmann (gregoa)]

On Mon, 22 Oct 2018 02:23:08 -0000, pauljohn32 wrote:

> On askubuntu.com, user asks about jabref error. On 18.10, jabref wont'
> start due to missing java modules. I answered that java 8 is required:
> https://askubuntu.com/a/1085678/495717. When java 11 is installed at
> same time, jabref won't start.

Now that openjdk-11 has arrived in Debian unstable, I can confirm the
problems.

> In my checking, one must actually remove java 11.

I doubt that. For me the following works:

JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/ jabref

If it doesn't please provide the output of

DEBUG_WRAPPER=1 JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/ jabref --debug

> I wonder if the version of java could be specified differently in the
> Ubuntu wrapping to solve this.

Right, seems like we have to do some java version finetuning again :/

Cheers,
gregor, one of the jabref maintainers in Debian

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[gregor herrmann (gregoa)]

The corresponding Debian bug is https://bugs.debian.org/912221
And it looks like Tony already has a fix almost ready.

Cheers,
gregor

[Launchpad Janitor (janitor)]

This bug was fixed in the package jabref - 3.8.2+ds-9

---------------
jabref (3.8.2+ds-9) unstable; urgency=medium

  * Invoke xjc from jaxb-xjc and drop build-dep on openjdk-8
  * Add build-dep on libxml-commons-resolver1.1-java
  * Replace mysql-connector JDBC driver with mariadb-client-java

 -- tony mancill <email address hidden> Wed, 07 Nov 2018 18:27:39 -0800

[Launchpad Janitor (janitor)]

This bug was fixed in the package jabref - 3.8.2+ds-12~18.04

---------------
jabref (3.8.2+ds-12~18.04) bionic; urgency=medium

  * Backport for OpenJDK 11. LP: #1814133.

jabref (3.8.2+ds-12) unstable; urgency=high

  * Add patch from upstream commit to fix CVE-2018-1000652: XML External
    Entity attack.
    Thanks to Moritz Muehlenhoff for the bug report. (Closes: #921772)

jabref (3.8.2+ds-11) unstable; urgency=medium

  * Add build dependency on libicu4j-java.
    Thanks to Santiago Vila for the bug report. (Closes: #918440)
  * Update years of packaging copyright.
  * Declare compliance with Debian Policy 4.3.0.

jabref (3.8.2+ds-10) unstable; urgency=medium

  * Build depend on librelaxng-datatype-java and add its jar to the
    classpath in debian/xjc.sh. (Closes: #915806)
  * Remove trailing whitespace from debian/*.
  * Add a lintian override (empty directory in source tree).
  * Add minimal headers to two patches.

jabref (3.8.2+ds-9) unstable; urgency=medium

  * Invoke xjc from jaxb-xjc and drop build-dep on openjdk-8
  * Add build-dep on libxml-commons-resolver1.1-java
  * Replace mysql-connector JDBC driver with mariadb-client-java

jabref (3.8.2+ds-8) unstable; urgency=medium

  * Add runtime dep on jaxb and update wrapper script for openjdk 11
    (Closes: #912221, LP: #1799106)
  * Include openjdk-8-jdk as a build-dep for the xjc binary (removed
    in openjdk-11) and patch build.gradle to compile using jaxb-api.
    Note that this package still uses default-jdk for the compilation
    itself. It cannot depend solely on openjdk-8-jdk, as Debian's
    gradle fails to run on that JDK. (Addresses FTBFS)
  * Bump Standards-Version to 4.2.1.

jabref (3.8.2+ds-7) unstable; urgency=medium

  * Add build-dep on libjsonp-java to builds against antlr4 version 4.6
    to address FTBFS (Closes: #906367)
  * Flesh-out CC-BY-3.0 license in debian/copyright

jabref (3.8.2+ds-6) unstable; urgency=medium

  * Wrapper will skip Java 9+ options when Java 8 runtime is detected
    (Closes: #900356)

jabref (3.8.2+ds-5) unstable; urgency=medium

  * Use workaround to start with JREs newer than Java8 (Closes: #893138)
    - Drop the runtime dependency on openjdk-8-jre
    - Set JABREF_JAVA_OPTS as per workaround documented by upstream
      (https://github.com/JabRef/jabref/issues/2594).
    - If this causes problems on a particular JRE, unset using:
      JABREF_JAVA_OPTS="" jabref ...
  * Use debhelper 11

jabref (3.8.2+ds-4) unstable; urgency=medium

  * Apply upstream patch for file perms (Closes: #857351)
  * Build with default-jdk
    - This resolves the build-time part of #893138
    - openjdk-8 is still required at runtime
  * Convert TR9401 catalog file to XML format for xjc/saxb 2.3
  * Add build-dep on libscram-java (needed by postgresql)
  * Add JDK9 swing patch
  * Update Vcs fields for migration from Alioth -> Salsa

 -- Matthias Klose <email address hidden> Tue, 26 Feb 2019 13:28:54 +0100