#1120 Jabref crashes when opening a file when using Java 7

[Postglock]

Hi,

I just reinstalled Kubuntu 12.10 on my computer, and attempted to run Jabref 2.9 as downloaded from the web page. Previously this worked fine for me. I've moved to a SSD + HDD setup, so I've had to change some paths.

Now, JabRef crashes when I select a file to open. It also crashes when I try to change the path for the external journal list (i.e. Options > Manage journal abbreviations > External files > Browse).

I've tried three versions of java. It fails on version 7 using both the official Sun Java and the OpenJDK Java. It does work on version 6 of the OpenJDK Java. I've copied the versions here:

$ java -version
java version "1.7.0_10"
Java(TM) SE Runtime Environment (build 1.7.0_10-b18)
Java HotSpot(TM) 64-Bit Server VM (build 23.6-b04, mixed mode)

$ java -version
java version "1.7.0_09"
OpenJDK Runtime Environment (IcedTea7 2.3.3) (7u9-2.3.3-0ubuntu1~12.10.1)
OpenJDK 64-Bit Server VM (build 23.2-b09, mixed mode)

$ java -version
java version "1.6.0_24"
OpenJDK Runtime Environment (IcedTea6 1.11.5) (6b24-1.11.5-0ubuntu1~12.10.1)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

I can open my file using OpenJDK 6, then quit and restart JabRef using either Java 7. The file is opened fine at startup, but attempting to open another file fails again.

The error message looks pretty similar for both Java 7's, and is pasted here:

$ Applications/JabRef.jar
Found 2 plugin(s):
- net.sf.jabref.core (jar:file:/home/postglock/Applications/JabRef-2.9.jar!/plugins/net.sf.jabref.core/plugin.xml)
- net.sf.jabref.export.misq (jar:file:/home/postglock/Applications/JabRef-2.9.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)

Opening: /HDD/postglock/Work/PhD/Archive/Application support/PhD reference library.bib

A fatal error has been detected by the Java Runtime Environment:

SIGSEGV (0xb) at pc=0x00007fc7297fd115, pid=29014, tid=140493002888960

JRE version: 7.0_09-b30

Java VM: OpenJDK 64-Bit Server VM (23.2-b09 mixed mode linux-amd64 compressed oops)

Problematic frame:

C [libmawt.so+0x41115] Java_com_sun_java_swing_plaf_gtk_GTKStyle_nativeGetPangoFontName+0x475

Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again

An error report file with more information is saved as:

/home/postglock/hs_err_pid29014.log

If you would like to submit a bug report, please include

instructions on how to reproduce the bug and visit:

https://bugs.launchpad.net/ubuntu/+source/openjdk-7/

Aborted (core dumped)

I've also attached /home/postglock/hs_err_pid29014.log as per the error message. I'm not exactly sure how to write the core dump, so please explain how if that would be useful.

[Oliver Kopp]

Please try Debian's JabRef package. Curently, it has not been migrated to Ubuntu, but surely will: http://packages.debian.org/experimental/all/jabref/download . Please let us know if that JabRef version works.

[Postglock]

I can't seem to get the link to work. All I get is "Error: two or more packages specified (download. jabref)".

[Oliver Kopp]

The dot (".") at the end of the link didn't belong to the link, but to the sentence. Sourceforge added the dot to the link. Now, I added a space. Please try again :)

[Postglock]

I ran into slightly different errors using both java 7's.

with Sun Java 7

$ jabref
[warning] /usr/bin/jabref: No java runtime was found
[warning] /usr/bin/jabref: No JAVA_CMD set for run_java, falling back to JAVA_CMD = java
log4j:WARN No appenders could be found for logger (org.java.plugin.ObjectFactory).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Found 2 plugin(s):
- net.sf.jabref.core (jar:file:/usr/share/jabref/JabRef-2.9.jar!/plugins/net.sf.jabref.core/plugin.xml)
- net.sf.jabref.export.misq (jar:file:/usr/share/jabref/JabRef-2.9.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)

Arguments passed on to running JabRef instance. Shutting down.

with OpenJDK 7

$ jabref
log4j:WARN No appenders could be found for logger (org.java.plugin.ObjectFactory).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Found 2 plugin(s):
- net.sf.jabref.core (jar:file:/usr/share/jabref/JabRef-2.9.jar!/plugins/net.sf.jabref.core/plugin.xml)
- net.sf.jabref.export.misq (jar:file:/usr/share/jabref/JabRef-2.9.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)

Arguments passed on to running JabRef instance. Shutting down.

[Oliver Kopp]

The string "Arguments passed on to running JabRef instance. Shutting down." indicates that another JabRef instance is running. Please ensure that no other instance is running (or disable "Remote operation" at Preferences/Advanced).

[Postglock]

Ah ok. I tried the debian version again, and it crashed at the same point (opening a file). I also tried the debian version with OpenJDK 6, and it worked fine.

I've attached the error/backtrace.