[Obo-discuss] OBO-Edit and Kubuntu

[Robinson, P. <pet...@ch...>]

Dear all,

I have just installed a kubuntu system (which in general is an extremely nice linux distribution), and installed Java 1.7 on it. Everything is working fine, except for OBO-Edit and Phenote. Both programs start without problems, but as soon as I actually do anything (for instance, enter a search term in the OBO edit window and begin the search), the loaded ontology simply disappears. I suppose this has something to do with the last line (I copied the messages from the command line)

(... open program, load ontology => no probs)

org.obo.dataadapter.OBOFileAdapter - Done parsing file
org.oboedit.gui.Preferences - Writing preferences to /home/peter/oboedit_config/config.xml
org.oboedit.gui.Preferences - Got memory string 1860M from option file /opt/OBO-Edit2/OBO-Edit.vmoptions
org.oboedit.gui.Preferences - updateInstallJLaunchers: adding -Xmx1860M to /opt/OBO-Edit2/OBO-Edit.vmoptions
org.oboedit.gui.Preferences - Could not update InstallJ launcher scripts
java.lang.InstantiationException: org.obo.datamodel.impl.DefaultLinkDatabase
Continuing ...
java.lang.RuntimeException: failed to evaluate: <unbound>=Class.new();
Continuing ..

I was not able to find anything about this in Google. Any ideas? Does this have to do with Java 7? Or is there something kubuntu-specific that anybody is aware of?

thanks Peter

PD Dr. med. Peter N. Robinson, MSc.
Institut für Medizinische Genetik und Humangenetik
Charité - Universitätsmedizin Berlin
Augustenburger Platz 1
13353 Berlin
Germany
+4930 450566006
Mobile: 0160 93769872
pet...@ch...
http://compbio.charite.de
http://www.human-phenotype-ontology.org
Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651