[ome-users] Error deploying OMERO 3.2 beta | jboss-log4j.xml

[» Ruben Alves]

Josh, it works now.
I've just change delete all preferences (.java), run OMERO as root, and 
the notice still appear, but OMERO starts perfectly.
I used binaries for PostgresSQL and Java (and not apt-get). And now, 
everything is working fine.
Thank you for your help.

//Ruben


Hi Ruben,

Oh boy. Sounds like we're not getting off the hook so easily. :)

First, I should mention that I couldn't reproduce this running as root
under Ubuntu. I get this message after deleting my preference
directories when I access preferences as root:

  root at millaboula <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users>:/etc/.java# java -cp /tmp prefs sys get
  17/03/2009 10:42:44 AM java.util.prefs.FileSystemPreferences$3 run
  INFO: Created system preferences directory in java.home.

» Ruben Alves writes:
 > Hi Josh, in fact I've already been in that site via Omero's 
 > troubleshooting page.
 > My /etc/.java is already world readable and writable, but the error 
 > continues.

Is there also a ".systemPrefs" directory under /etc/.java ? And what
about in ~/.java? There should be a .userPrefs directory.

 > Omero is running as root in a Debian Lenny Linux.
 > I've installed Java with apt-get and downloaded the official installer. 
 > In both, I got the same error.
 > The problem is because of this error, OMERO don't even start.
 > 
 > To deploy omero I use this script:
 > 
 > omero:/var/omero-Beta3.2# cat deploy_server.sh
 > #!/bin/bash
 > 
 > export http_proxy="http://proxy.lan:8080/" <http://proxy.lan:8080/%22>
 > export JBOSS_HOME=/var/omero-Beta3.2/jboss-4.2.3.GA/
 > cd /var/omero-Beta3.2/omero
 > java omero deploy
 > $JBOSS_HOME/bin/run.sh
 > 
 > Now, I really don't know how to fix this problem.

One thing mentioned on another bug:

  http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4666397

is to set where the properties get created:

  There is another system property 'java.util.prefs.systemRoot' whose
  default is '/etc/.java'.  Set it on the command line to a directory
  that you have control of and make a .systemPrefs directory in it.

I tested:

  java -Djava.util.prefs.userRoot=/tmp -cp /tmp prefs sys set a 1

This is probably preferable to making everything read/write world,
since some applications may put private information in there.
 
 > Regards

Good luck!
~Josh.

P.S. can you pass along the server logs, possibly after adding:

  set -x

to the top of run.sh?

 > » Ruben Alves writes:
 >  > Hi all,
 > 
 > Hi Ruben,
 > 
 >  > I've just moved to the last omero public release. But I can't > 
 > understand why I can't deploy omero without this error:
 >  > > 17:54:59,383 INFO  [Log4jService$URLWatchTimerTask] Configuring 
 > from > URL: resource:jboss-log4j.xml
 >  > 2009-03-16 17:55:53,697 ERROR [STDERR] (main) 16/Mar/2009 17:55:53 > 
 > java.util.prefs.FileSystemPreferences$7 run
 >  > WARNING: Prefs file removed in background 
 > /root/.java/.userPrefs/prefs.xml
 >  > 2009-03-16 17:55:53,719 ERROR [STDERR] (main) 16/Mar/2009 17:55:53 > 
 > java.util.prefs.FileSystemPreferences$7 run
 >  > WARNING: Prefs file removed in background 
 > /etc/.java/.systemPrefs/prefs.xml
 >  > > I will appreciate any kind of help.
 > 
 > First, is everything working properly despite the error messages? In
 > our experience, this is an issue with how Java was installed, but is
 > not detrimental to the server's functioning. This bug in the Sun
 > database might be of interest:
 > 
 > http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4751177
 > 
 >  > My best regards,
 >  > > //Ruben
 > 
 > Hope that helps,
 > ~Josh
 > 
 > -- 
 > Ruben Alves 
 > 
 > System Analyst 
 > USI @ Instituto de Medicina Molecular
 > Edifício Egas Moniz 
 > Av. Prof. Egas Moniz 1649-028 Lisboa Portugal 
 > tel: 217999411 ext 47026
 > rubenalves at fm.ul.pt <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users>



-- 
Ruben Alves 

System Analyst 
USI @ Instituto de Medicina Molecular
Edifício Egas Moniz 
Av. Prof. Egas Moniz 1649-028 Lisboa Portugal 
tel: 217999411 ext 47026
rubenalves at fm.ul.pt