Re: Bug#814901: jabref: at start jabref hangs with the error message "No appenders could be found for logger ..."
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"
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 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
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".
----------------------------------------------------------------------------------------------------
>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
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.
The second time it hang again with the usual output.
$ 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)
====================================================================================================
> I'm cc'ing the java team's mailing list, maybe someone has an idea
> there.
Thanks.
====================================================================================================
[...]
> > 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
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*"
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)
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.
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.
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