Jabref (2.11.1, 2.11b3, 2.10) hangs after Java upgrade on Ubuntu 15.10

[David Peebles]

All three versions of Jabref hang (after starting up OK, reading the database and selecting an entry), say when editing a file link or some other operation. Once this happens all buttons are inactive and I have to kill the process. This started today after Java got upgraded.

Linux version 4.2.0-18-generic (buildd@lgw01-38) (gcc version 5.2.1 20151010 (Ubuntu 5.2.1-22ubuntu2) ) #22-Ubuntu SMP Fri Nov 6 18:25:50 UTC 2015 (Ubuntu 4.2.0-18.22-generic 4.2.3)

java version "1.7.0_91"
OpenJDK Runtime Environment (IcedTea 2.6.3) (7u91-2.6.3-0ubuntu0.15.10.1)
OpenJDK 64-Bit Server VM (build 24.91-b01, mixed mode)

[Oliver Kopp (kopp-dev)]

At https://github.com/JabRef/jabref/issues/393#issuecomment-159959483, a jstack thread dump has been posted.

[Launchpad Janitor (janitor)]

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

[Samuel thibault (samuel-thibault)]

Please see the end of https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=797595 : awt is currently not calling XInitThreads(), and libxcb is thus not thread-safe. Jabref happens to be using threads, so all kinds of funky things is to be expected. The patch proposed there will probably fix the issue.

[Oliver Kopp (kopp-dev)]

The current solution seems to be either to go to Preferences -> Advanced and then choose the "MetalLookAndFeel" or to edit /etc/java-7-openjdk/accessibility.properties and to disable assistive_technologies=org.GNOME.Accessibility.AtkWrapper.

[Aere Greenway (aere)]

The KeyMusician Keyboard application (installed via a Debian package) was working with no problems. After applying updates (which included an update to the Open Java JRE), it now hangs during initialization.

There were times in the past where I was running with it, and suddenly my X-windows session abruptly died. This problem seemed to happen when I was using the GTK+ look-and-feel.

I will gather more information, to see if the GTK+ look-and-feel affects this problem.

Surprisingly, the same application (JAR-file) works okay when launched via Java Web Start (icedtea-netx).

[Aere Greenway (aere)]

I ran another test, and confirmed that the problem is connected to using the GTK+ look-and-feel.

I discovered that if the configuration is changed so that it starts up with any of the following look-and-feels, it initializes normally:

Metal
Nimbus
CDE/Motif

After initializing with one of the above, I was able to change successfully to the GTK+ look-and-feel. But when I saved the configuration so that it will initialize next time using the GTK+ look-and-feel, the next time I tried to initialize it, it hung during initialization (at the point where it changes to the configured look-and-feel).

[Launchpad Janitor (janitor)]

This bug was fixed in the package jabref - 3.6+ds-1

---------------
jabref (3.6+ds-1) unstable; urgency=medium

  * New upstream version. Fixes the following bugs:
    - "New version and new web address" (Closes: #810725)
    - "interface opens, but no menus and no action" (Closes: #846918)
    - "arXiv.org: Search only works using the paper ID." (Closes: #627857)
    - "Unusable after 'missing comma between two fields'" (Closes: #727114)
    - "problems with openjdk-8, awt, and threads" (Closes: #814901)
    - "Jabref duplicated file ?" (Closes: #563649)
    - "jabref not performing online search" (LP: #1449414)
    - "trying to do searches online" (LP: #1641602)
    - "Jabref hangs after Java upgrade" (LP: #1520294)
    - "Jabref fails to open" (LP: #1570068)
  * Build system is now gradle-based and leverages gradle-debian-helper.
    Build-deps, debian/rules, wrapper script, and patches have been
    completely reworked.
  * Notable new patches:
    - Disable "Lookup DOI" feature, which was causing JabRef to hang.
    - Diff-highlighting during "Merge Entries" is disabled due to license
      issues that prevent the distribution of the java-diff-tools library.
  * Update debian/copyright for upstream license changes.
  * Drop lintian overrides (duplicate-word).
  * Update documentation (debian/README.Debian, debian/README.source,
    debian/jabref.1, debian/jabref.bug-presubj) to match new release and
    drop outdated bits.
  * Use debhelper compatibility level 10.

 -- tony mancill <email address hidden> Thu, 08 Dec 2016 20:04:34 -0800