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[protege-discussion] Weird sudden problem in ubuntu 13.04

André Luiz Tietböhl Ramos andreltramos at gmail.com
Thu Jun 27 13:30:17 PDT 2013


Hello,

My computer, which runs 13.04, began to show the problem below all of a
sudden:

andreltr at sigmatech:/opt/Protege_4.3$ ./run.sh 
ERROR: Bundle org.protege.common [1] Error starting
file:/opt/Protege_4.3/bundles/org.protege.common.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.common [1]: Unable to resolve 1.0: missing requirement [1.0]
osgi.wiring.package;
(&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0)))
org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.common [1]: Unable to resolve 1.0: missing requirement [1.0]
osgi.wiring.package;
(&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0))
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle org.protege.editor.core.application [7] Error starting
file:/opt/Protege_4.3/bundles/org.protege.editor.core.application.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.editor.core.application [7]: Unable to resolve 7.0: missing
requirement [7.0] osgi.wiring.package;
(&(osgi.wiring.package=com.jgoodies.looks)(version>=2.2.1)) [caused by:
Unable to resolve 1.0: missing requirement [1.0] osgi.wiring.package;
(&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0))])
org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.editor.core.application [7]: Unable to resolve 7.0: missing
requirement [7.0] osgi.wiring.package;
(&(osgi.wiring.package=com.jgoodies.looks)(version>=2.2.1)) [caused by:
Unable to resolve 1.0: missing requirement [1.0] osgi.wiring.package;
(&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0))]
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
Error:  Could not parse XML contribution for
"org.eclipse.equinox.registry//plugin.xml". Any contributed extensions
and extension points will be ignored.
ERROR: Bundle org.protege.owl.rdf [9] Error starting
file:/opt/Protege_4.3/plugins/org.protege.owl.rdf.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.owl.rdf [9]: Unable to resolve 9.0: missing requirement
[9.0] osgi.wiring.package;
(&(osgi.wiring.package=javax.imageio)(version>=0.0.0)))
org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.owl.rdf [9]: Unable to resolve 9.0: missing requirement
[9.0] osgi.wiring.package;
(&(osgi.wiring.package=javax.imageio)(version>=0.0.0))
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle org.semanticweb.owl.owlapi [10] Error starting
file:/opt/Protege_4.3/plugins/org.semanticweb.owl.owlapi.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
org.semanticweb.owl.owlapi [10]: Unable to resolve 10.0: missing
requirement [10.0] osgi.wiring.package;
(&(osgi.wiring.package=javax.swing)(version>=0.0.0)))
org.osgi.framework.BundleException: Unresolved constraint in bundle
org.semanticweb.owl.owlapi [10]: Unable to resolve 10.0: missing
requirement [10.0] osgi.wiring.package;
(&(osgi.wiring.package=javax.swing)(version>=0.0.0))
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle org.protege.ontograf [11] Error starting
file:/opt/Protege_4.3/plugins/org.protege.ontograf.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.ontograf [11]: Unable to resolve 11.0: missing requirement
[11.0] osgi.wiring.package; (osgi.wiring.package=javax.imageio))
org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.ontograf [11]: Unable to resolve 11.0: missing requirement
[11.0] osgi.wiring.package; (osgi.wiring.package=javax.imageio)
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle uk.ac.manchester.cs.owl.factplusplus [12] Error starting
file:/opt/Protege_4.3/plugins/uk.ac.manchester.cs.owl.factplusplus.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
uk.ac.manchester.cs.owl.factplusplus [12]: Unable to resolve 12.0:
missing requirement [12.0] osgi.wiring.package;
(osgi.wiring.package=org.apache.log4j) [caused by: Unable to resolve
1.0: missing requirement [1.0] osgi.wiring.package;
(&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0))])
org.osgi.framework.BundleException: Unresolved constraint in bundle
uk.ac.manchester.cs.owl.factplusplus [12]: Unable to resolve 12.0:
missing requirement [12.0] osgi.wiring.package;
(osgi.wiring.package=org.apache.log4j) [caused by: Unable to resolve
1.0: missing requirement [1.0] osgi.wiring.package;
(&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0))]
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle org.protege.editor.owl.diff [13] Error starting
file:/opt/Protege_4.3/plugins/org.protege.editor.owl.diff.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.editor.owl.diff [13]: Unable to resolve 13.0: missing
requirement [13.0] osgi.wiring.package;
(osgi.wiring.package=javax.swing))
org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.editor.owl.diff [13]: Unable to resolve 13.0: missing
requirement [13.0] osgi.wiring.package;
(osgi.wiring.package=javax.swing)
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle ca.uvic.cs.chisel.cajun [14] Error starting
file:/opt/Protege_4.3/plugins/ca.uvic.cs.chisel.cajun.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
ca.uvic.cs.chisel.cajun [14]: Unable to resolve 14.0: missing
requirement [14.0] osgi.wiring.package;
(&(osgi.wiring.package=javax.imageio)(version>=0.0.0)))
org.osgi.framework.BundleException: Unresolved constraint in bundle
ca.uvic.cs.chisel.cajun [14]: Unable to resolve 14.0: missing
requirement [14.0] osgi.wiring.package;
(&(osgi.wiring.package=javax.imageio)(version>=0.0.0))
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle org.protege.owl.diff [15] Error starting
file:/opt/Protege_4.3/plugins/org.protege.owl.diff.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.owl.diff [15]: Unable to resolve 15.0: missing requirement
[15.0] osgi.wiring.package; (osgi.wiring.package=org.apache.log4j)
[caused by: Unable to resolve 1.0: missing requirement [1.0]
osgi.wiring.package;
(&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0))])
org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.owl.diff [15]: Unable to resolve 15.0: missing requirement
[15.0] osgi.wiring.package; (osgi.wiring.package=org.apache.log4j)
[caused by: Unable to resolve 1.0: missing requirement [1.0]
osgi.wiring.package;
(&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0))]
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle org.protege.editor.owl.rdf [16] Error starting
file:/opt/Protege_4.3/plugins/org.protege.editor.owl.rdf.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.editor.owl.rdf [16]: Unable to resolve 16.0: missing
requirement [16.0] osgi.wiring.package;
(&(osgi.wiring.package=javax.swing)(version>=0.0.0)))
org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.editor.owl.rdf [16]: Unable to resolve 16.0: missing
requirement [16.0] osgi.wiring.package;
(&(osgi.wiring.package=javax.swing)(version>=0.0.0))
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle org.protege.editor.owl [17] Error starting
file:/opt/Protege_4.3/plugins/org.protege.editor.owl.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.editor.owl [17]: Unable to resolve 17.0: missing requirement
[17.0] osgi.wiring.package;
(&(osgi.wiring.package=com.clarkparsia.owlapi.explanation)(version>=3.2.4)) [caused by: Unable to resolve 10.0: missing requirement [10.0] osgi.wiring.package; (&(osgi.wiring.package=javax.swing)(version>=0.0.0))])
org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.editor.owl [17]: Unable to resolve 17.0: missing requirement
[17.0] osgi.wiring.package;
(&(osgi.wiring.package=com.clarkparsia.owlapi.explanation)(version>=3.2.4)) [caused by: Unable to resolve 10.0: missing requirement [10.0] osgi.wiring.package; (&(osgi.wiring.package=javax.swing)(version>=0.0.0))]
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle org.coode.dlquery [18] Error starting
file:/opt/Protege_4.3/plugins/org.coode.dlquery.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
org.coode.dlquery [18]: Unable to resolve 18.0: missing requirement
[18.0] osgi.wiring.package; (osgi.wiring.package=org.apache.log4j)
[caused by: Unable to resolve 1.0: missing requirement [1.0]
osgi.wiring.package;
(&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0))])
org.osgi.framework.BundleException: Unresolved constraint in bundle
org.coode.dlquery [18]: Unable to resolve 18.0: missing requirement
[18.0] osgi.wiring.package; (osgi.wiring.package=org.apache.log4j)
[caused by: Unable to resolve 1.0: missing requirement [1.0]
osgi.wiring.package;
(&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0))]
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle org.coode.owlviz [19] Error starting
file:/opt/Protege_4.3/plugins/org.coode.owlviz.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
org.coode.owlviz [19]: Unable to resolve 19.0: missing requirement
[19.0] osgi.wiring.package; (osgi.wiring.package=javax.swing))
org.osgi.framework.BundleException: Unresolved constraint in bundle
org.coode.owlviz [19]: Unable to resolve 19.0: missing requirement
[19.0] osgi.wiring.package; (osgi.wiring.package=javax.swing)
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle uk.ac.manchester.cs.owl.explanation [20] Error starting
file:/opt/Protege_4.3/plugins/org.protege.explanation.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
uk.ac.manchester.cs.owl.explanation [20]: Unable to resolve 20.0:
missing requirement [20.0] osgi.wiring.package;
(osgi.wiring.package=org.apache.log4j) [caused by: Unable to resolve
1.0: missing requirement [1.0] osgi.wiring.package;
(&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0))])
org.osgi.framework.BundleException: Unresolved constraint in bundle
uk.ac.manchester.cs.owl.explanation [20]: Unable to resolve 20.0:
missing requirement [20.0] osgi.wiring.package;
(osgi.wiring.package=org.apache.log4j) [caused by: Unable to resolve
1.0: missing requirement [1.0] osgi.wiring.package;
(&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0))]
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle org.protege.editor.owl.codegeneration [21] Error starting
file:/opt/Protege_4.3/plugins/org.protege.editor.owl.codegeneration.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.editor.owl.codegeneration [21]: Unable to resolve 21.0:
missing requirement [21.0] osgi.wiring.package;
(osgi.wiring.package=javax.swing))
org.osgi.framework.BundleException: Unresolved constraint in bundle
org.protege.editor.owl.codegeneration [21]: Unable to resolve 21.0:
missing requirement [21.0] osgi.wiring.package;
(osgi.wiring.package=javax.swing)
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
ERROR: Bundle org.semanticweb.HermiT [22] Error starting
file:/opt/Protege_4.3/plugins/org.semanticweb.HermiT.jar
(org.osgi.framework.BundleException: Unresolved constraint in bundle
org.semanticweb.HermiT [22]: Unable to resolve 22.0: missing requirement
[22.0] osgi.wiring.bundle;
(&(osgi.wiring.bundle=org.protege.editor.core.application)(bundle-version>=4.1.0)) [caused by: Unable to resolve 7.0: missing requirement [7.0] osgi.wiring.package; (&(osgi.wiring.package=com.jgoodies.looks)(version>=2.2.1)) [caused by: Unable to resolve 1.0: missing requirement [1.0] osgi.wiring.package; (&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0))]])
org.osgi.framework.BundleException: Unresolved constraint in bundle
org.semanticweb.HermiT [22]: Unable to resolve 22.0: missing requirement
[22.0] osgi.wiring.bundle;
(&(osgi.wiring.bundle=org.protege.editor.core.application)(bundle-version>=4.1.0)) [caused by: Unable to resolve 7.0: missing requirement [7.0] osgi.wiring.package; (&(osgi.wiring.package=com.jgoodies.looks)(version>=2.2.1)) [caused by: Unable to resolve 1.0: missing requirement [1.0] osgi.wiring.package; (&(osgi.wiring.package=org.w3c.dom)(version>=0.0.0))]]
    at
org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3818)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:1868)
    at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1191)
    at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:295)
    at java.lang.Thread.run(Thread.java:724)
...

After this it hung up.  Below is the part of my .bashrc that I think may
be relevant,

PATH=
$PATH:/opt/gams:/opt/cmucl/bin:/opt/MagicDraw_UML/bin:/opt/CPNTools:/opt/Protege:/opt/bin:/opt/android-sdk:/opt/android-sdk/tools:/opt/android-sdk/platform-tools:/opt/smlnj:/opt/smlnj/bin:/opt/smlnj/lib
export PATH
CLASSPATH=
$CLASSPATH:/usr/local/lib/postgres/postgresql-8.4-703.jdbc4.jar:/opt/jade/lib/jade.jar:/opt/jade/lib/commons-codec/commons-codec-1.3.jar:/opt/jade/:/opt/jade/lib/:/opt/jade/lib/jadeTools.jar:/opt/jade/lib/Base64.jar:/opt/jade/lib/http.jar:/opt/Protege_4.1/plugins/beangenerator_4.1.jar:/opt/Protege_4.2_beta/plugins/beangenerator.jar:/opt/JSDAI_Standalone/JSDAI:/opt/JSDAI_Standalone/JSDAI/lib:/opt/jena/lib:/opt/jess:/opt/jess/jess.jar
export CLASSPATH
export JAVA_HOME=/usr/lib/jvm/java-7-oracle
export JAVA=$JAVA_HOME:$JAVA
export PATH=$PATH:$JAVA_HOME/bin

Any help greatly appreciated.


-- 
André Luiz Tietböhl Ramos

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