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Bug#814901: jabref: at start jabref hangs with the error message "No appenders could be found for logger ..."

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gregor herrmann

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Feb 16, 2016, 11:39:32 AM2/16/16

Control: tag -1 + unreproducible
Control: severity -1 important

On Tue, 16 Feb 2016 12:34:32 +0100, Josef Atmin wrote:

> Package: jabref
> Version: 2.10+ds-5
> Severity: grave
> Justification: renders package unusable
>
> Dear Maintainer,

Hallo Josef!

Sorry to hear that you have problems with JabRef, and thanks for this
excellent bug report!

First of all, I'm unfortunately unable to reproduce it, JabRef still
works fine for me, with OpenJDK 8. Therefore I'm lowering the
severity of the bug.

> 1. When starting jabref I get the following error message and it hangs at the welcome screen or aborts.
>
> 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.export.misq (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)
> - net.sf.jabref.core (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.core/plugin.xml)
>
> 2. I have read http://logging.apache.org/log4j/1.2/faq.html#noconfig and some
> blog entries on the internet to figure out how to configure log4j, but without
> success since I have no clue how java works.

The log4j warnings are harmless; there are there since forever, and I
also get them before JabRef starts successfully.

> 4. When trying to file a bug report I got the info

Yay! Thanks for this debugging session.

> 6. I did the debug test mentioned above for all four available versions.
>
> prompt> DEBUG_WRAPPER=1 JAVA_HOME=/usr/lib/jvm/java-1.5.0-gcj-4.9-amd64/ jabref
> prompt> DEBUG_WRAPPER=1 JAVA_HOME=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/ jabref

The failure here is no surprise, cf.:

> WARNING: You are running Java version 1.6 or lower (1.5.0 to be exact).
> JabRef needs at least a Java Runtime Environment 1.6 or higher.
> JabRef should not start properly and output an error message
> (probably java.lang.UnsupportedClassVersionError ... (Unsupported major.minor version 49.0)
> See http://jabref.sf.net/faq.php for more information.
>
> WARNING: You are not running a Java version from Oracle (or Sun Microsystems).
> Your java vendor is: Free Software Foundation, Inc.
> If JabRef crashes please consider switching to an Oracle Java Runtime.
> See http://jabref.sf.net/faq.php for more information.

and also the package dependencies.

> ============================================================================================================
>
> prompt> DEBUG_WRAPPER=1 JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64/ jabref
>
> [debug] /usr/bin/jabref: Using provided JAVA_HOME = '/usr/lib/jvm/java-7-openjdk-amd64/'
> [debug] /usr/bin/jabref: Found JAVA_HOME = '/usr/lib/jvm/java-7-openjdk-amd64/'
> [debug] /usr/bin/jabref: Found JAVA_CMD = '/usr/lib/jvm/java-7-openjdk-amd64//bin/java'
> [debug] /usr/bin/jabref: Environment variable CLASSPATH is ''
> [debug] /usr/bin/jabref: Runnning /usr/lib/jvm/java-7-openjdk-amd64//bin/java -classpath /usr/share/java/jabref.jar:/usr/share/java/JPFCodeGenerator-rt.jar:/usr/share/java/antlr.jar:/usr/share/java/antlr3.jar:/usr/share/java/commons-logging.jar:/usr/share/java/glazedlists.jar:/usr/share/java/jempbox.jar:/usr/share/java/jgoodies-common.jar:/usr/share/java/jgoodies-forms.jar:/usr/share/java/jgoodies-looks.jar:/usr/share/java/jpf.jar:/usr/share/java/jpf-boot.jar:/usr/share/java/microba.jar:/usr/share/java/mysql-connector-java.jar:/usr/share/java/pdfbox.jar:/usr/share/java/postgresql.jar:/usr/share/java/spin.jar net.sf.jabref.JabRefMain
> 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-2.10.jar!/plugins/net.sf.jabref.core/plugin.xml)
> - net.sf.jabref.export.misq (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)

This _should_ work (I don't have OpenJDK 7 installed any more) ...

> prompt> DEBUG_WRAPPER=1 JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/ jabref
>
> [debug] /usr/bin/jabref: Using provided JAVA_HOME = '/usr/lib/jvm/java-8-openjdk-amd64/'
> [debug] /usr/bin/jabref: Found JAVA_HOME = '/usr/lib/jvm/java-8-openjdk-amd64/'
> [debug] /usr/bin/jabref: Found JAVA_CMD = '/usr/lib/jvm/java-8-openjdk-amd64//bin/java'
> [debug] /usr/bin/jabref: Environment variable CLASSPATH is ''
> [debug] /usr/bin/jabref: Runnning /usr/lib/jvm/java-8-openjdk-amd64//bin/java -classpath /usr/share/java/jabref.jar:/usr/share/java/JPFCodeGenerator-rt.jar:/usr/share/java/antlr.jar:/usr/share/java/antlr3.jar:/usr/share/java/commons-logging.jar:/usr/share/java/glazedlists.jar:/usr/share/java/jempbox.jar:/usr/share/java/jgoodies-common.jar:/usr/share/java/jgoodies-forms.jar:/usr/share/java/jgoodies-looks.jar:/usr/share/java/jpf.jar:/usr/share/java/jpf-boot.jar:/usr/share/java/microba.jar:/usr/share/java/mysql-connector-java.jar:/usr/share/java/pdfbox.jar:/usr/share/java/postgresql.jar:/usr/share/java/spin.jar net.sf.jabref.JabRefMain
> 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.export.misq (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)
> - net.sf.jabref.core (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.core/plugin.xml)
>
> Xlib: extension "XInputExtension" missing on display ":0".

Ha! Here's an extra line, and that's the difference to my output.
Now we just need to find out what's missing / different on your
system, so that java can't connect to the X server.

(But then, your test with OpenJDK 7 should work?)

Do other java programs work for you? Which window manager are you
using?

I'm cc'ing the java team's mailing list, maybe someone has an idea
there.

> 9. Downloaded java for Linux from http://www.java.com/en/download/linux_manual.jsp and installed it.
>
> root> cd /usr/lib/jvm/
> root> tar xvf jre-8u73-linux-x64.tar.gz
>
> 10. Tested this version
>
> prompt> DEBUG_WRAPPER=1 JAVA_HOME=/usr/lib/jvm/jre1.8.0_73/ jabref
>
> [debug] /usr/bin/jabref: Using provided JAVA_HOME = '/usr/lib/jvm/jre1.8.0_73/'
> [debug] /usr/bin/jabref: Found JAVA_HOME = '/usr/lib/jvm/jre1.8.0_73/'
> [debug] /usr/bin/jabref: Found JAVA_CMD = '/usr/lib/jvm/jre1.8.0_73//bin/java'
> [debug] /usr/bin/jabref: Environment variable CLASSPATH is ''
> [debug] /usr/bin/jabref: Runnning /usr/lib/jvm/jre1.8.0_73//bin/java -classpath /usr/share/java/jabref.jar:/usr/share/java/JPFCodeGenerator-rt.jar:/usr/share/java/antlr.jar:/usr/share/java/antlr3.jar:/usr/share/java/commons-logging.jar:/usr/share/java/glazedlists.jar:/usr/share/java/jempbox.jar:/usr/share/java/jgoodies-common.jar:/usr/share/java/jgoodies-forms.jar:/usr/share/java/jgoodies-looks.jar:/usr/share/java/jpf.jar:/usr/share/java/jpf-boot.jar:/usr/share/java/microba.jar:/usr/share/java/mysql-connector-java.jar:/usr/share/java/pdfbox.jar:/usr/share/java/postgresql.jar:/usr/share/java/spin.jar net.sf.jabref.JabRefMain
> Feb 16, 2016 12:23:35 PM java.util.prefs.FileSystemPreferences$1 run
> INFO: Created user preferences directory.
> 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.export.misq (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)
> - net.sf.jabref.core (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.core/plugin.xml)

Hm, nothing here about Xlib ...

> 11. Provide the openjdk info for the bugreport.
>
> prompt> dpkg -l "openjdk*"
>
> Desired=Unknown/Install/Remove/Purge/Hold
> | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
> ||/ Name Version Architecture Description
> +++-==============-============-============-=================================
> un openjdk-6-jdk <none> <none> (no description available)
> un openjdk-6-jre <none> <none> (no description available)
> un openjdk-6-jre- <none> <none> (no description available)
> ii openjdk-7-jre: 7u95-2.6.4-1 amd64 OpenJDK Java runtime, using Hotsp
> ii openjdk-7-jre- 7u95-2.6.4-1 amd64 OpenJDK Java runtime, using Hotsp
> un openjdk-7-jre- <none> <none> (no description available)
> ii openjdk-8-jre: 8u72-b15-2 amd64 OpenJDK Java runtime, using Hotsp
> ii openjdk-8-jre- 8u72-b15-2 amd64 OpenJDK Java runtime, using Hotsp
> un openjdk-8-jre- <none> <none> (no description available)

For comparison:

% dpkg -l "openjdk*"
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name Version Architecture Description
+++-===============================-====================-====================-====================================================================
un openjdk-6-jdk <none> <none> (no description available)
un openjdk-6-jre <none> <none> (no description available)
un openjdk-6-jre-headless <none> <none> (no description available)
un openjdk-7-jre <none> <none> (no description available)
un openjdk-8-demo <none> <none> (no description available)
ii openjdk-8-jdk:amd64 8u72-b15-2 amd64 OpenJDK Development Kit (JDK)
ii openjdk-8-jre:amd64 8u72-b15-2 amd64 OpenJDK Java runtime, using Hotspot JIT
ii openjdk-8-jre-headless:amd64 8u72-b15-2 amd64 OpenJDK Java runtime, using Hotspot JIT (headless)
un openjdk-8-jre-jamvm <none> <none> (no description available)
un openjdk-8-source <none> <none> (no description available)

So the differences are that
- I have only OpenJDK 8
- I also have openjdk-8-jdk

> 12. Gave up!

Thanks for you perseverance!

Cheers,
gregor

--
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: :' : Debian GNU/Linux user, admin, and developer - https://www.debian.org/
`. `' Member of VIBE!AT & SPI, fellow of the Free Software Foundation Europe
`- NP: Bevinda: Fado

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Josef Atmin

unread,

Feb 16, 2016, 5:10:02 PM2/16/16

Dear Gregor,

thanks a lot for the quick reply.

On Tue, Feb 16, 2016 at 05:05:54PM +0100, gregor herrmann wrote:
> Control: tag -1 + unreproducible
> Control: severity -1 important
>
> On Tue, 16 Feb 2016 12:34:32 +0100, Josef Atmin wrote:
>
> > Package: jabref
> > Version: 2.10+ds-5
> > Severity: grave
> > Justification: renders package unusable
> >
> > Dear Maintainer,
>
> Hallo Josef!
>
> Sorry to hear that you have problems with JabRef, and thanks for this
> excellent bug report!
>
> First of all, I'm unfortunately unable to reproduce it, JabRef still
> works fine for me, with OpenJDK 8. Therefore I'm lowering the
> severity of the bug.
>

[...]

====================================================================================================

> The log4j warnings are harmless; there are there since forever, and I
> also get them before JabRef starts successfully.

Ok! Good to know, before I spend too much time trying to solve that.

====================================================================================================

[...]

> > prompt> DEBUG_WRAPPER=1 JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/ jabref
> >
> > [debug] /usr/bin/jabref: Using provided JAVA_HOME = '/usr/lib/jvm/java-8-openjdk-amd64/'
> > [debug] /usr/bin/jabref: Found JAVA_HOME = '/usr/lib/jvm/java-8-openjdk-amd64/'
> > [debug] /usr/bin/jabref: Found JAVA_CMD = '/usr/lib/jvm/java-8-openjdk-amd64//bin/java'
> > [debug] /usr/bin/jabref: Environment variable CLASSPATH is ''
> > [debug] /usr/bin/jabref: Runnning /usr/lib/jvm/java-8-openjdk-amd64//bin/java -classpath /usr/share/java/jabref.jar:/usr/share/java/JPFCodeGenerator-rt.jar:/usr/share/java/antlr.jar:/usr/share/java/antlr3.jar:/usr/share/java/commons-logging.jar:/usr/share/java/glazedlists.jar:/usr/share/java/jempbox.jar:/usr/share/java/jgoodies-common.jar:/usr/share/java/jgoodies-forms.jar:/usr/share/java/jgoodies-looks.jar:/usr/share/java/jpf.jar:/usr/share/java/jpf-boot.jar:/usr/share/java/microba.jar:/usr/share/java/mysql-connector-java.jar:/usr/share/java/pdfbox.jar:/usr/share/java/postgresql.jar:/usr/share/java/spin.jar net.sf.jabref.JabRefMain
> > 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.export.misq (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)
> > - net.sf.jabref.core (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.core/plugin.xml)
> >
> > Xlib: extension "XInputExtension" missing on display ":0".
>
> Ha! Here's an extra line, and that's the difference to my output.
> Now we just need to find out what's missing / different on your
> system, so that java can't connect to the X server.
>
> (But then, your test with OpenJDK 7 should work?)

I have tried this particular test again five times and did not get the
Xlib message again.

====================================================================================================

> Do other java programs work for you?

Hm, I don't know. How would I find out? What are common other java programs?

Ok, I looked a bit on the internet and wanted to write a little mini
program in java. I figured I need the javac compiler. It is not
installed on my computer, and it was not in the Debian unstable
repository under that name either. aptitude told me that the package
javacc contains javac, so I installed javacc, but the command javac
was still not available, so I gave up on that for the time being.

$ javacc -version
Java Compiler Compiler Version 5.0 (Parser Generator)
(type "javacc" with no arguments for help)
Last argument "-version" is not a filename.

$ javac -version
bash: javac: command not found

$ dpkg -l "javac*"

Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name Version Architecture Description

+++-==============================================-============================-============================-==================================================================================================
ii javacc 5.0-5 all Parser generator for use with Java
un javacc-doc <none> <none> (no description available)

====================================================================================================

> Which window manager are you using?

I use cinnamon.

$ dpkg -l "cinnamon"

+++-==============================================-============================-============================-==================================================================================================
ii cinnamon 2.8.6-1 amd64 Innovative and comfortable desktop

I have then logged out and logged in gnome. Then I ran jabref. The first time it actually worked and I got the following messages.

$ 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.export.misq (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)
- net.sf.jabref.core (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.core/plugin.xml)

Gtk-Message: Failed to load module "canberra-gtk-module"
Opening: /home/wiskott/Literatur/Bibtexs/WiskottGroup.bib
Opening: /home/wiskott/Literatur/Bibtexs/Hippocampus.bib
Opening: /home/wiskott/Literatur/Bibtexs/GraphicalModels.bib
Opening: /home/wiskott/Literatur/Bibtexs/SlowFeatureAnalysis.bib
Could not get key binding for "Open folder"

----------------------------------------------------------------------------------------------------

The second time it did not work. It hang with the welcome screen, just like under cinnamon, and the messages were as follows.

wiskott@garlic:~$ jabref

----------------------------------------------------------------------------------------------------

From then on it did not work anymore and I did not get the Xlib
message anymore. I also killed all the java processes hanging around
in the backgroud, which were created by jabref, and that did not
change anything.

$ killall -9 java

====================================================================================================

I then rebooted and logged into gnome again.

The first time a started jabref it actually crashed (and did not hang as usually) with the following messages.

$ jabref

java: Fatal IO error 11 (Resource temporarily unavailable) on X server :0.

The second time it hang again with the usual output.

$ jabref

====================================================================================================

> I'm cc'ing the java team's mailing list, maybe someone has an idea
> there.

Thanks.

====================================================================================================

[...]

Ok, I am back in cinnamon now.

I deinstalled openjdk-7 and installed openjdk-8-jdk

# aptitude purge openjdk-7-jre openjdk-7-jre-headless
The following packages will be REMOVED:
openjdk-7-jre{ap} openjdk-7-jre-headless{ap}
[...]
# aptitude install openjdk-8-jdk
The following NEW packages will be installed:
libice-dev{a} libpthread-stubs0-dev{a} libsm-dev{a} libx11-dev{a} libx11-doc{a} libxau-dev{a} libxcb1-dev{a} libxdmcp-dev{a} libxt-dev{a} openjdk-8-jdk x11proto-core-dev{a} x11proto-input-dev{a}
x11proto-kb-dev{a} xorg-sgml-doctools{a} xtrans-dev{a}
[...]
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javah to provide /usr/bin/javah (javah) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode

The following now looks like on your computer.

# dpkg -l "openjdk*"

un openjdk-6-jdk <none> <none> (no description available)
un openjdk-6-jre <none> <none> (no description available)
un openjdk-6-jre-headless <none> <none> (no description available)
un openjdk-7-jre <none> <none> (no description available)
un openjdk-8-demo <none> <none> (no description available)
ii openjdk-8-jdk:amd64 8u72-b15-2 amd64 OpenJDK Development Kit (JDK)
ii openjdk-8-jre:amd64 8u72-b15-2 amd64 OpenJDK Java runtime, using Hotspot JIT
ii openjdk-8-jre-headless:amd64 8u72-b15-2 amd64 OpenJDK Java runtime, using Hotspot JIT (headless)
un openjdk-8-jre-jamvm <none> <none> (no description available)
un openjdk-8-source <none> <none> (no description available)

First run of jabref crashed with

$ jabref

java: Fatal IO error 11 (Resource temporarily unavailable) on X server :0.

Second run of jabref hung again with the usual output.

====================================================================================================

Gave up ;-)

I hope all that gives you a bit more information to work with.

Best wishes,

Josef.

gregor herrmann

unread,

Feb 16, 2016, 6:20:04 PM2/16/16

Control: forwarded -1 https://github.com/JabRef/jabref/issues/393

On Tue, 16 Feb 2016 22:50:14 +0100, Josef Atmin wrote:

> Dear Gregor,
> thanks a lot for the quick reply.

Thanks for looking further into this issue!

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

> > >
> > > Xlib: extension "XInputExtension" missing on display ":0".
> > Ha! Here's an extra line, and that's the difference to my output.
> > Now we just need to find out what's missing / different on your
> > system, so that java can't connect to the X server.
> > (But then, your test with OpenJDK 7 should work?)
> I have tried this particular test again five times and did not get the
> Xlib message again.

Hm. Maybe because there was still a java process lingering around?

> > Do other java programs work for you?
> Hm, I don't know. How would I find out? What are common other java programs?

Depends on what you like :)
freemind, josm, tuxguitar are some that I use.

`apt-cache rdepends default-jre' might give you some ideas.

> Ok, I looked a bit on the internet and wanted to write a little mini
> program in java. I figured I need the javac compiler. It is not
> installed on my computer, and it was not in the Debian unstable
> repository under that name either.

"My" javac is /usr/bin/javac -> /etc/alternatives/javac -> /usr/lib/jvm/java-8-openjdk-amd64/bin/javac
(from the openjdk-8-jdk package). But I guess installing another
package with software written in Java is easier.

> > Which window manager are you using?
> I use cinnamon.

Ok, I'm not aware of any specific problems with cinnamon and java but
who knows.

> I have then logged out and logged in gnome. Then I ran jabref. The first time it actually worked and I got the following messages.
>
> $ 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.export.misq (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)
> - net.sf.jabref.core (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.core/plugin.xml)
>
> Gtk-Message: Failed to load module "canberra-gtk-module"
> Opening: /home/wiskott/Literatur/Bibtexs/WiskottGroup.bib
> Opening: /home/wiskott/Literatur/Bibtexs/Hippocampus.bib
> Opening: /home/wiskott/Literatur/Bibtexs/GraphicalModels.bib
> Opening: /home/wiskott/Literatur/Bibtexs/SlowFeatureAnalysis.bib
> Could not get key binding for "Open folder"

Cool. The Gtk warning seems to come from Gnome but should be
harmless, the rest looks like when I start JabRef.

> ----------------------------------------------------------------------------------------------------
>
> The second time it did not work. It hang with the welcome screen, just like under cinnamon, and the messages were as follows.
>
> wiskott@garlic:~$ 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.export.misq (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)
> - net.sf.jabref.core (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.core/plugin.xml)
>
> Xlib: extension "XInputExtension" missing on display ":0".
>
> ----------------------------------------------------------------------------------------------------

Oh, again troubles with the X server.

> I then rebooted and logged into gnome again.
>
> The first time a started jabref it actually crashed (and did not hang as usually) with the following messages.
>
> $ 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.export.misq (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)
> - net.sf.jabref.core (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.core/plugin.xml)
>
> java: Fatal IO error 11 (Resource temporarily unavailable) on X server :0.

Again, something between Java and X.

> > So the differences are that
> > - I have only OpenJDK 8
> > - I also have openjdk-8-jdk
>
> Ok, I am back in cinnamon now.
> I deinstalled openjdk-7 and installed openjdk-8-jdk

Thanks for trying this as well.

> First run of jabref crashed with
>
> $ 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.export.misq (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)
> - net.sf.jabref.core (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.core/plugin.xml)
>
> java: Fatal IO error 11 (Resource temporarily unavailable) on X server :0.

So X again. Hm.

> I hope all that gives you a bit more information to work with.

It's certainly not a lack of information from your side that leaves
me a bit clueless :) Currently I think that the problem lies not with
JabRef but I have no idea what's happening between java and X on your
machine. - My hopes still lie in the Java team and their expertise :)

Or this: After some searching I found https://bugs.debian.org/802701
which sounds quite similar. And even mentions JabRef ... with the
upstream ticket at https://github.com/JabRef/jabref/issues/393 . And
the Ubuntu bug at
https://bugs.launchpad.net/ubuntu/+source/jabref/+bug/1520294

The GitHub issue contains a workaround (changing the look&feel),
maybe this works for you too? (Same info in the Launchpad bug.)

Cheers,
gregor

--
.''`. Homepage https://info.comodo.priv.at/ - OpenPGP key 0xBB3A68018649AA06
: :' : Debian GNU/Linux user, admin, and developer - https://www.debian.org/
`. `' Member of VIBE!AT & SPI, fellow of the Free Software Foundation Europe

`- NP: The Beatles: Love me do

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Josef Atmin

unread,

Feb 18, 2016, 12:40:03 PM2/18/16

Dear Gregor,

thanks a lot for your help. I now have a workaround, see below. It was great to work with you :-)

On Wed, Feb 17, 2016 at 12:11:47AM +0100, gregor herrmann wrote:
[...]
====================================================================================================

> > > > prompt> DEBUG_WRAPPER=1 JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/ jabref
> > > >
> > > > Xlib: extension "XInputExtension" missing on display ":0".
> > > Ha! Here's an extra line, and that's the difference to my output.
> > > Now we just need to find out what's missing / different on your
> > > system, so that java can't connect to the X server.
> > > (But then, your test with OpenJDK 7 should work?)
> > I have tried this particular test again five times and did not get the
> > Xlib message again.
>
> Hm. Maybe because there was still a java process lingering around?

I tried this test a couple of times more:

1) I get the error message

java: Fatal IO error 11 (Resource temporarily unavailable) on X server :0.

apart from the usual other erro messages and jabref crashed.

2) dito

3) It actually started and worked.

4) It hung.

Then I killed all java processes: $ killall -9 java

5) It actually started and worked.

6) It actually started and worked.

7) It hung.

Then I killed all java processes: $ killall -9 java

8) It actually started and worked.

9) It actually started and worked.

10) It hung.

Then I killed all java processes: $ killall -9 java

Ok, so much statistics for now. I am actually surprised that it
worked a couple of time. So far it normally did not work at all.

====================================================================================================

> > > Do other java programs work for you?
> > Hm, I don't know. How would I find out? What are common other java programs?
>
> Depends on what you like :)
> freemind, josm, tuxguitar are some that I use.
>
> `apt-cache rdepends default-jre' might give you some ideas.

'libreoffice' runs without problems.

====================================================================================================

> > Ok, I looked a bit on the internet and wanted to write a little mini
> > program in java. I figured I need the javac compiler. It is not
> > installed on my computer, and it was not in the Debian unstable
> > repository under that name either.
>
> "My" javac is /usr/bin/javac -> /etc/alternatives/javac -> /usr/lib/jvm/java-8-openjdk-amd64/bin/javac
> (from the openjdk-8-jdk package). But I guess installing another
> package with software written in Java is easier.

Ok, I found it. Now, it is all like that for my computer too.
However, I did not bother writing a little java programm anymore,
because 'libreoffice' runs ok and shows that java is ok in principle.

====================================================================================================

[...]

> > I hope all that gives you a bit more information to work with.
>
> It's certainly not a lack of information from your side that leaves
> me a bit clueless :) Currently I think that the problem lies not with
> JabRef but I have no idea what's happening between java and X on your
> machine. - My hopes still lie in the Java team and their expertise :)

====================================================================================================

> Or this: After some searching I found https://bugs.debian.org/802701
> which sounds quite similar. And even mentions JabRef ... with the
> upstream ticket at https://github.com/JabRef/jabref/issues/393 . And
> the Ubuntu bug at
> https://bugs.launchpad.net/ubuntu/+source/jabref/+bug/1520294
>
> The GitHub issue contains a workaround (changing the look&feel),
> maybe this works for you too? (Same info in the Launchpad bug.)

Ok, I commented out the line

assistive_technologies=org.GNOME.Accessibility.AtkWrapper

in file

/etc/java-8-openjdk/accessibility.properties

and then jabref started 10 times in a row with the usual error messages

$ 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.export.misq (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)
- net.sf.jabref.core (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.core/plugin.xml)

but without any problems. Then I uncommented the line again and
jabref started to not work reliably again. So that is a workaround
for me.

----------------------------------------------------------------------------------------------------

Then I tried the other solution. I went to Options -> Preferences ->
Advanced and checked the tickbox 'Use other look and feel \\ Class
name: com.jgoodies.plaf.plastic.Plastic3DLookAndFeel'. That
workaround also worked, jabref started and apparently runs fine but
with some more error messages:

java.lang.ClassNotFoundException: com.jgoodies.plaf.plastic.Plastic3DLookAndFeel
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at javax.swing.SwingUtilities.loadSystemClass(SwingUtilities.java:1874)
at javax.swing.UIManager.setLookAndFeel(UIManager.java:582)
at net.sf.jabref.JabRef.setLookAndFeel(JabRef.java:669)
at net.sf.jabref.JabRef.openWindow(JabRef.java:726)
at net.sf.jabref.JabRef.<init>(JabRef.java:201)
at net.sf.jabref.JabRef.main(JabRef.java:84)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at net.sf.jabref.JabRefMain.main(Unknown Source)

Removing the tick mark again leads to the old unreliable behavior.

====================================================================================================

Ok, that solves the problem for me. Thanks a lot for your help.

Best wishes,

Josef.

Josef Atmin

unread,

Feb 19, 2016, 1:00:05 PM2/19/16

PS: Maybe I should add: I got my unstable distribution by first installing stable and then do first an upgrade and then a dist-upgrade.

gregor herrmann

unread,

Feb 23, 2016, 12:00:03 PM2/23/16

Control: tag -1 - unreproducible
Control: severity -1 normal
Control: retitle -1 jabref: problems with openjdk-8, awt, and threads
# probably: Control: reassign -1 openjdk-8
# Control: merge -1 $some_openjdk-8_bug -1 # maybe #798131

On Thu, 18 Feb 2016 18:23:26 +0100, Josef Atmin wrote:

> Dear Gregor,
> thanks a lot for your help. I now have a workaround, see below. It was great to work with you :-)

I'm glad you've found a woring workaround, thanks for your patience!

> I tried this test a couple of times more:

[..]

> Ok, so much statistics for now. I am actually surprised that it
> worked a couple of time. So far it normally did not work at all.

Yeah, that matches what Samuel wrote in
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=802701#25 about
race conditions due to the usage of threads.

> > > > Do other java programs work for you?
> > > Hm, I don't know. How would I find out? What are common other java programs?
> > Depends on what you like :)
> > freemind, josm, tuxguitar are some that I use.
> > `apt-cache rdepends default-jre' might give you some ideas.
> 'libreoffice' runs without problems.

Hm, maybe not the best example, since AFAIK only parts of LO need/use
Java. But nevermind.

> > Or this: After some searching I found https://bugs.debian.org/802701
> > which sounds quite similar. And even mentions JabRef ... with the
> > upstream ticket at https://github.com/JabRef/jabref/issues/393 . And
> > the Ubuntu bug at
> > https://bugs.launchpad.net/ubuntu/+source/jabref/+bug/1520294
> >
> > The GitHub issue contains a workaround (changing the look&feel),
> > maybe this works for you too? (Same info in the Launchpad bug.)
>
> Ok, I commented out the line
>
> assistive_technologies=org.GNOME.Accessibility.AtkWrapper
>
> in file
>
> /etc/java-8-openjdk/accessibility.properties
>
> and then jabref started 10 times in a row with the usual error messages
>
> $ 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.export.misq (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.export.misq/plugin.xml)
> - net.sf.jabref.core (jar:file:/usr/share/jabref/JabRef-2.10.jar!/plugins/net.sf.jabref.core/plugin.xml)
>
> but without any problems. Then I uncommented the line again and
> jabref started to not work reliably again. So that is a workaround
> for me.

Yay \o/

> Then I tried the other solution. I went to Options -> Preferences ->
> Advanced and checked the tickbox 'Use other look and feel \\ Class
> name: com.jgoodies.plaf.plastic.Plastic3DLookAndFeel'. That
> workaround also worked, jabref started and apparently runs fine but
> with some more error messages:

Thanks for trying this as well.

`- NP: Cat Stevens: Crazy

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