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.
