Bug#890905: jabref: does not launch

Mauricio Calvao mocalvao at gmail.com
Fri Feb 23 11:46:14 UTC 2018 

The results of your suggested 3 commands are:

$ DEBUG_WRAPPER=1 jabref --debug            (does not launch):

[debug] /usr/bin/jabref: Picking up the JVM designated by the alternatives
system:
[debug] /usr/bin/jabref:   JAVA_HOME = '/usr/lib/jvm/java-9-openjdk-amd64'
[debug] /usr/bin/jabref: Found JAVA_HOME =
'/usr/lib/jvm/java-9-openjdk-amd64'
[debug] /usr/bin/jabref: Found JAVA_CMD =
'/usr/lib/jvm/java-9-openjdk-amd64/bin/java'
[debug] /usr/bin/jabref: Environment variable CLASSPATH is ''
[debug] /usr/bin/jabref: Runnning
/usr/lib/jvm/java-9-openjdk-amd64/bin/java  -classpath
/usr/share/java/jabref.jar:/usr/share/java/bcprov.jar:/usr/share/java/antlr3-runtime.jar:/usr/share/java/antlr4-runtime.jar:/usr/share/java/com.android.json.jar:/usr/share/java/commons-cli.jar:/usr/share/java/commons-codec.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/commons-logging.jar:/usr/share/java/fontbox.jar:/usr/share/java/glazedlists.jar:/usr/share/java/guava.jar:/usr/share/java/httpasyncclient.jar:/usr/share/java/httpclient.jar:/usr/share/java/httpcore.jar:/usr/share/java/httpcore-nio.jar:/usr/share/java/httpmime.jar:/usr/share/java/java-string-similarity.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/jhlabs-filters.jar:/usr/share/java/jsoup.jar:/usr/share/java/juh.jar:/usr/share/java/jurt.jar:/usr/share/java/log4j-api.jar:/usr/share/java/log4j-core.jar:/usr/share/java/log4j-jcl.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/ridl.jar:/usr/share/java/spin.jar:/usr/share/java/swingx.jar:/usr/share/java/swing-layout.jar:/usr/share/java/unirest-java.jar:/usr/share/java/unoil.jar
net.sf.jabref.JabRefMain --debug
08:41:47.135 [AWT-EventQueue-0] ERROR
net.sf.jabref.FallbackExceptionHandler - Uncaught exception Occurred in
Thread[AWT-EventQueue-0,6,main]
java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
        at
net.sf.jabref.logic.importer.ImportFormatReader.resetImportFormats(ImportFormatReader.java:56)
~[JabRef-3.8.2.jar:?]
        at net.sf.jabref.JabRefMain.start(JabRefMain.java:78)
~[JabRef-3.8.2.jar:?]
        at net.sf.jabref.JabRefMain.lambda$main$0(JabRefMain.java:40)
~[JabRef-3.8.2.jar:?]
        at
java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313) ~[?:?]
        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:764) ~[?:?]
        at java.awt.EventQueue.access$500(EventQueue.java:97) ~[?:?]
        at java.awt.EventQueue$3.run(EventQueue.java:717) ~[?:?]
        at java.awt.EventQueue$3.run(EventQueue.java:711) ~[?:?]
        at java.security.AccessController.doPrivileged(Native Method) ~[?:?]
        at
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
~[?:?]
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:734) ~[?:?]
        at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:199)
[?:?]
        at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
[?:?]
        at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
[?:?]
        at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) [?:?]
        at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [?:?]
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
[?:?]
Caused by: java.lang.ClassNotFoundException: javax.xml.bind.JAXBException
        at
jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)
~[?:?]
        at
jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:185)
~[?:?]
        at java.lang.ClassLoader.loadClass(ClassLoader.java:496) ~[?:?]
        ... 17 more

$ DEBUG_WRAPPER=1 JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/ jabref
--debug      (does launch!!!)
[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/bcprov.jar:/usr/share/java/antlr3-runtime.jar:/usr/share/java/antlr4-runtime.jar:/usr/share/java/com.android.json.jar:/usr/share/java/commons-cli.jar:/usr/share/java/commons-codec.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/commons-logging.jar:/usr/share/java/fontbox.jar:/usr/share/java/glazedlists.jar:/usr/share/java/guava.jar:/usr/share/java/httpasyncclient.jar:/usr/share/java/httpclient.jar:/usr/share/java/httpcore.jar:/usr/share/java/httpcore-nio.jar:/usr/share/java/httpmime.jar:/usr/share/java/java-string-similarity.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/jhlabs-filters.jar:/usr/share/java/jsoup.jar:/usr/share/java/juh.jar:/usr/share/java/jurt.jar:/usr/share/java/log4j-api.jar:/usr/share/java/log4j-core.jar:/usr/share/java/log4j-jcl.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/ridl.jar:/usr/share/java/spin.jar:/usr/share/java/swingx.jar:/usr/share/java/swing-layout.jar:/usr/share/java/unirest-java.jar:/usr/share/java/unoil.jar
net.sf.jabref.JabRefMain --debug
08:42:38.000 [AWT-EventQueue-0] DEBUG
net.sf.jabref.logic.logging.JabRefLogger - Showing debug messages
08:42:38.001 [AWT-EventQueue-0] DEBUG net.sf.jabref.cli.ArgumentProcessor -
Finished export
08:42:38.006 [AWT-EventQueue-0] WARN  net.sf.jabref.JabRefGUI - There seem
to be problems with OpenJDK and the default GTK Look&Feel. Using Metal L&F
instead. Change to another L&F with caution.
08:42:38.024 [AWT-EventQueue-0] INFO
net.sf.jabref.logic.importer.OpenDatabase - Opening:
/home/orca/Dropbox/work/papers/collaboration/emf_and_the_like/manuscript/emf_and_the_like.bib
08:42:38.105 [AWT-EventQueue-0] DEBUG
net.sf.jabref.logic.importer.OpenDatabase - Synchronized special fields
based on keywords
08:42:38.106 [AWT-EventQueue-0] INFO
net.sf.jabref.logic.importer.OpenDatabase - Opening:
/home/orca/Dropbox/work/papers/collaboration/reference_frames/manuscript/reference_frames.bib
08:42:38.111 [AWT-EventQueue-0] DEBUG
net.sf.jabref.logic.importer.OpenDatabase - Synchronized special fields
based on keywords
08:42:38.111 [AWT-EventQueue-0] WARN
net.sf.jabref.logic.importer.OpenDatabase - Empty BibTeX key: N/A:
"Proceedings of the {I}nternational ... (Grouping may not work for this
entry.)
08:42:38.150 [AWT-EventQueue-0] DEBUG net.sf.jabref.JabRefGUI -
Initializing frame
08:42:51.063 [AWT-EventQueue-0] DEBUG net.sf.jabref.JabRefGUI - Finished
adding panels
08:43:09.219 [FileUpdateMonitor] DEBUG
net.sf.jabref.collab.FileUpdateMonitor - FileUpdateMonitor has been
interrupted. Terminating...
java.lang.InterruptedException: sleep interrupted
        at java.lang.Thread.sleep(Native Method) ~[?:1.8.0_151]
        at
net.sf.jabref.collab.FileUpdateMonitor.run(FileUpdateMonitor.java:43)
[JabRef-3.8.2.jar:?]
        at
net.sf.jabref.JabRefExecutorService$NamedRunnable.run(JabRefExecutorService.java:96)
[JabRef-3.8.2.jar:?]
        at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
[?:1.8.0_151]
        at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
[?:1.8.0_151]
        at java.lang.Thread.run(Thread.java:748) [?:1.8.0_151]


$ DEBUG_WRAPPER=1 JAVA_HOME=/usr/lib/jvm/java-9-openjdk-amd64/ jabref
--debug        (does not launch)

[debug] /usr/bin/jabref: Using provided JAVA_HOME =
'/usr/lib/jvm/java-9-openjdk-amd64/'
[debug] /usr/bin/jabref: Found JAVA_HOME =
'/usr/lib/jvm/java-9-openjdk-amd64/'
[debug] /usr/bin/jabref: Found JAVA_CMD =
'/usr/lib/jvm/java-9-openjdk-amd64//bin/java'
[debug] /usr/bin/jabref: Environment variable CLASSPATH is ''
[debug] /usr/bin/jabref: Runnning
/usr/lib/jvm/java-9-openjdk-amd64//bin/java  -classpath
/usr/share/java/jabref.jar:/usr/share/java/bcprov.jar:/usr/share/java/antlr3-runtime.jar:/usr/share/java/antlr4-runtime.jar:/usr/share/java/com.android.json.jar:/usr/share/java/commons-cli.jar:/usr/share/java/commons-codec.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/commons-logging.jar:/usr/share/java/fontbox.jar:/usr/share/java/glazedlists.jar:/usr/share/java/guava.jar:/usr/share/java/httpasyncclient.jar:/usr/share/java/httpclient.jar:/usr/share/java/httpcore.jar:/usr/share/java/httpcore-nio.jar:/usr/share/java/httpmime.jar:/usr/share/java/java-string-similarity.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/jhlabs-filters.jar:/usr/share/java/jsoup.jar:/usr/share/java/juh.jar:/usr/share/java/jurt.jar:/usr/share/java/log4j-api.jar:/usr/share/java/log4j-core.jar:/usr/share/java/log4j-jcl.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/ridl.jar:/usr/share/java/spin.jar:/usr/share/java/swingx.jar:/usr/share/java/swing-layout.jar:/usr/share/java/unirest-java.jar:/usr/share/java/unoil.jar
net.sf.jabref.JabRefMain --debug
08:45:16.713 [AWT-EventQueue-0] ERROR
net.sf.jabref.FallbackExceptionHandler - Uncaught exception Occurred in
Thread[AWT-EventQueue-0,6,main]
java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
        at
net.sf.jabref.logic.importer.ImportFormatReader.resetImportFormats(ImportFormatReader.java:56)
~[JabRef-3.8.2.jar:?]
        at net.sf.jabref.JabRefMain.start(JabRefMain.java:78)
~[JabRef-3.8.2.jar:?]
        at net.sf.jabref.JabRefMain.lambda$main$0(JabRefMain.java:40)
~[JabRef-3.8.2.jar:?]
        at
java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313) ~[?:?]
        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:764) ~[?:?]
        at java.awt.EventQueue.access$500(EventQueue.java:97) ~[?:?]
        at java.awt.EventQueue$3.run(EventQueue.java:717) ~[?:?]
        at java.awt.EventQueue$3.run(EventQueue.java:711) ~[?:?]
        at java.security.AccessController.doPrivileged(Native Method) ~[?:?]
        at
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
~[?:?]
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:734) ~[?:?]
        at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:199)
[?:?]
        at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
[?:?]
        at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
[?:?]
        at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) [?:?]
        at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [?:?]
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
[?:?]
Caused by: java.lang.ClassNotFoundException: javax.xml.bind.JAXBException
        at
jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)
~[?:?]
        at
jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:185)
~[?:?]
        at java.lang.ClassLoader.loadClass(ClassLoader.java:496) ~[?:?]
        ... 17 more


On Fri, Feb 23, 2018 at 7:14 AM, gregor herrmann <gregoa at debian.org> wrote:

> On Tue, 20 Feb 2018 10:13:46 -0300, Mauricio Calvao wrote:
>
> > I just clicked the jabref icon, from the KDE applications launch
> > menu and also tried just plain typing jabref in a terminal.
> >
> > After clicking the icon, a temporary widget on the lower panel
> > showed up, but then vanished and jabref's gui never was spawned.
> > After the command line trial, the following message arose:
> >
> > 10:00:18.907 [AWT-EventQueue-0] ERROR net.sf.jabref.FallbackExceptionHandler
> - Uncaught exception Occurred in Thread[AWT-EventQueue-0,6,main]
> > java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
> >         at net.sf.jabref.logic.importer.ImportFormatReader.
> resetImportFormats(ImportFormatReader.java:56) ~[JabRef-3.8.2.jar:?]
> >         at net.sf.jabref.JabRefMain.start(JabRefMain.java:78)
> ~[JabRef-3.8.2.jar:?]
> >         at net.sf.jabref.JabRefMain.lambda$main$0(JabRefMain.java:40)
> ~[JabRef-3.8.2.jar:?]
> >         at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
> ~[?:?]
> >         at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:764)
> ~[?:?]
> >         at java.awt.EventQueue.access$500(EventQueue.java:97) ~[?:?]
> >         at java.awt.EventQueue$3.run(EventQueue.java:717) ~[?:?]
> >         at java.awt.EventQueue$3.run(EventQueue.java:711) ~[?:?]
> >         at java.security.AccessController.doPrivileged(Native Method)
> ~[?:?]
> >         at java.security.ProtectionDomain$JavaSecurityAccessImpl.
> doIntersectionPrivilege(ProtectionDomain.java:89) ~[?:?]
> >         at java.awt.EventQueue.dispatchEvent(EventQueue.java:734) ~[?:?]
> >         at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:199)
> [?:?]
> >         at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
> [?:?]
> >         at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
> [?:?]
> >         at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
> [?:?]
> >         at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
> [?:?]
> >         at java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
> [?:?]
> > Caused by: java.lang.ClassNotFoundException:
> javax.xml.bind.JAXBException
> >         at jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)
> ~[?:?]
> >         at jdk.internal.loader.ClassLoaders$AppClassLoader.
> loadClass(ClassLoaders.java:185) ~[?:?]
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:496) ~[?:?]
> >         ... 17 more
>
> Thanks for your bug report. This is indeed not the expected outcome
> :)
>
> As JabRef still works for me, we need to find out what's different
> for you.
>
> > ii  openjdk-8-jre [java8-runtime]     8u151-b12-1
> > ii  openjdk-9-jre [java8-runtime]     9.0.1+11-1
> > ii  oracle-java8-jdk [java8-runtime]  8u11
>
> > ii  openjdk-8-jdk:amd64                   8u151-b12-1 amd64
>      OpenJDK Development Kit (JDK)
> > ii  openjdk-8-jdk-headless:amd64          8u151-b12-1 amd64
>      OpenJDK Development Kit (JDK) (headless)
> > ii  openjdk-8-jre:amd64                   8u151-b12-1 amd64
>      OpenJDK Java runtime, using Hotspot JIT
> > ii  openjdk-8-jre-headless:amd64          8u151-b12-1 amd64
>      OpenJDK Java runtime, using Hotspot JIT (headless)
> > ii  openjdk-9-jdk:amd64                   9.0.1+11-1 amd64
>      OpenJDK Development Kit (JDK)
> > ii  openjdk-9-jdk-headless:amd64          9.0.1+11-1 amd64
>      OpenJDK Development Kit (JDK) (headless)
> > ii  openjdk-9-jre:amd64                   9.0.1+11-1 amd64
>      OpenJDK Java runtime, using Hotspot JIT
> > ii  openjdk-9-jre-headless:amd64          9.0.1+11-1 amd64
>      OpenJDK Java runtime, using Hotspot JIT (headless)
>
> > java - auto mode
> >   link best version is /usr/lib/jvm/java-9-openjdk-amd64/bin/java
> >   link currently points to /usr/lib/jvm/java-9-openjdk-amd64/bin/java
> >   link java is /usr/bin/java
> >   slave java.1.gz is /usr/share/man/man1/java.1.gz
> > /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java - priority 1081
> >   slave java.1.gz: /usr/lib/jvm/java-8-openjdk-
> amd64/jre/man/man1/java.1.gz
> > /usr/lib/jvm/java-9-openjdk-amd64/bin/java - priority 1091
> >   slave java.1.gz: /usr/lib/jvm/java-9-openjdk-amd64/man/man1/java.1.gz
> > /usr/lib/jvm/oracle-java8-jdk-amd64/jre/bin/java - priority 318
> >   slave java.1.gz: /usr/lib/jvm/oracle-java8-jdk-
> amd64/man/man1/java.1.gz
>
> This looks like you're using openjdk-9 for running JabRef.
>
> Could you please try:
>
> DEBUG_WRAPPER=1 jabref --debug
>
> DEBUG_WRAPPER=1 JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/ jabref
> --debug
>
> DEBUG_WRAPPER=1 JAVA_HOME=/usr/lib/jvm/java-9-openjdk-amd64/ jabref
> --debug
>
>
> Cheers,
> gregor
>
>
> --
>  .''`.  https://info.comodo.priv.at -- Debian Developer
> https://www.debian.org
>  : :' : OpenPGP fingerprint D1E1 316E 93A7 60A8 104D  85FA BB3A 6801 8649
> AA06
>  `. `'  Member VIBE!AT & SPI Inc. -- Supporter Free Software Foundation
> Europe
>    `-
>
> -----BEGIN PGP SIGNATURE-----
>
> iQKTBAEBCgB9FiEE0eExbpOnYKgQTYX6uzpoAYZJqgYFAlqP6ZdfFIAAAAAALgAo
> aXNzdWVyLWZwckBub3RhdGlvbnMub3BlbnBncC5maWZ0aGhvcnNlbWFuLm5ldEQx
> RTEzMTZFOTNBNzYwQTgxMDREODVGQUJCM0E2ODAxODY0OUFBMDYACgkQuzpoAYZJ
> qgZ9wQ/8D4oocSvaaLxFT2JCUw22YM2buew9VmHNUHAC8XNV3Bc1RDypXzSf8KL2
> F+VG/XwyJZ1mB/q9aeg9IeMPcwevkSrPo/gswmih/blE5seYbOW9CFkf5MflRwV2
> PFYqDkQgiedLocKvenkbFS8FDHobEY3qFqN70zVzGiPhHd8Da/R7uHouCJfxalZw
> d9drsgICvqhE9a9FLqPUwfQY1T8sTpGa6ptjUOaygg2QVJzPvd9bG3o+/5OCJEZH
> rLD6HbjqyQLzTh2wdhbSGygTI+xO4MmXWTDeH0XmIUzoPNHYO/9doyHlUiEMS45h
> gEMGmEhk5sVaaFChwBf+kAROejb8dKvq/0epWS29GfPkh/iJklZWB0g4LD3dJJQu
> 6bIohJtFgxTcvNmW08p6j1LY7wgEnZFoAKffkrFBQPVewOuKb2gGo0WHeP2888jY
> 69FceFLoA4mx3uMJpo5+0SuZMCcq/T9rUFyEfUkBinX7kTznE3rWQUh2G156D+6X
> YcCxVZs7YiNMC2bTTY0Lo+c3qRK6hJxCpUqG8MXs97CoNhXFPI7MRinNzPNtMwTF
> k+b11DVEVDs7RyT8M8IuFwv7oOARQGRVdT51vwvZbHO0u3R8HqEhl0hO0uk3dOEc
> mbymvsXKEcnlzWfw/eM9r5XewINO5WKtLVt5ba6ywsaTL5G2U/I=
> =xy77
> -----END PGP SIGNATURE-----
>
>


-- 
#######################################
Prof. Mauricio Ortiz Calvao
Federal University of Rio de Janeiro
Institute of Physics, P O Box 68528
CEP 21941-972 Rio de Janeiro, RJ
Brazil

Email: orca at if.ufrj.br
Phone: (55)(21)39387483
Homepage: http://www.if.ufrj.br/~orca
#######################################
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/pkg-java-maintainers/attachments/20180223/203cb5d2/attachment-0001.html>

More information about the pkg-java-maintainers mailing list