Arch Linux

Protege 5.2.0-5 does not start, installed in Manjaro. Here's what shows up when I use the command line.


Additional info:

$ inxi -S
System: Kernel: 4.20.17-1-MANJARO x86_64 bits: 64 Desktop: KDE Plasma 5.15.3 Distro: Manjaro Linux

When I download the package manually, unzip it, and start from command line (i.e. run.sh), Protege looks okay.

Steps to reproduce:

-- From the Pamac installed version --

$ ./protege
CompileCommand: exclude javax/swing/text/GlyphView.getBreakSpot
********************************************************************************
** Protege **
********************************************************************************

----------------- Initialising and Starting the OSGi Framework -----------------
FrameworkFactory Class: org.apache.felix.framework.FrameworkFactory

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.felix.framework.util.SecureAction (file:/usr/share/java/protege/bin/org.apache.felix.main.jar) to method java.net.URLClassLoader.addURL(java.net.URL)
WARNING: Please consider reporting this to the maintainers of org.apache.felix.framework.util.SecureAction
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
The OSGi framework has been initialised
------------------------------- Starting Bundles -------------------------------
Starting bundle org.protege.common
Starting bundle org.eclipse.equinox.supplement
Starting bundle org.eclipse.equinox.common
Starting bundle org.eclipse.equinox.registry
Starting bundle org.protege.editor.core.application
Starting bundle ch.qos.logback.classic
Starting bundle org.apache.commons.io
Starting bundle org.protege.common
Starting bundle org.eclipse.equinox.registry
Starting bundle jul.to.slf4j
Starting bundle slf4j.api
Not starting bundle com.google.inject.multibindings explicitly because it is a fragment bundle.
Starting bundle org.apache.servicemix.bundles.aopalliance
Starting bundle com.google.inject
Starting bundle ch.qos.logback.core
Starting bundle com.google.guava
Starting bundle org.eclipse.equinox.supplement
Not starting bundle com.google.inject.assistedinject explicitly because it is a fragment bundle.
Starting bundle org.jsr-305
Starting bundle org.protege.editor.core.application
Starting bundle org.semanticweb.owl.owlapi
Starting bundle org.eclipse.equinox.common
Starting bundle org.apache.servicemix.bundles.javax-inject
Starting bundle org.protege.editor.owl
Starting bundle log4j.over.slf4j
Error starting file:/usr/share/java/protege/bundles/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.slf4j)(version>=1.7.0)(!(version>=2.0.0))) [caused by: Unable to resolve 9.0: missing requirement [9.0] osgi.ee; (&(osgi.ee=JavaSE)(version=1.5.0))]
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4002) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2045) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304) [org.apache.felix.main.jar:na]
at java.base/java.lang.Thread.run(Thread.java:844) [na:na]
Error starting file:/usr/share/java/protege/bundles/org.eclipse.equinox.supplement.jar
org.osgi.framework.BundleException: Unresolved constraint in bundle org.eclipse.equinox.supplement [2]: Unable to resolve 2.0: missing requirement [2.0] osgi.ee; (|(&(osgi.ee=JavaSE)(version=1.4.0))(&(osgi.ee=CDC/Foundation)(version=1.0.0))(&(osgi.ee=JavaSE)(version=1.3.0)))
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4002) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2045) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304) [org.apache.felix.main.jar:na]
at java.base/java.lang.Thread.run(Thread.java:844) [na:na]
Error starting file:/usr/share/java/protege/bundles/org.eclipse.equinox.common.jar
org.osgi.framework.BundleException: Unresolved constraint in bundle org.eclipse.equinox.common [3]: Unable to resolve 3.0: missing requirement [3.0] osgi.wiring.package; (osgi.wiring.package=org.eclipse.osgi.framework.log) [caused by: Unable to resolve 2.0: missing requirement [2.0] osgi.ee; (|(&(osgi.ee=JavaSE)(version=1.4.0))(&(osgi.ee=CDC/Foundation)(version=1.0.0))(&(osgi.ee=JavaSE)(version=1.3.0)))]
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4002) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2045) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304) [org.apache.felix.main.jar:na]
at java.base/java.lang.Thread.run(Thread.java:844) [na:na]
Error starting file:/usr/share/java/protege/bundles/org.eclipse.equinox.registry.jar
org.osgi.framework.BundleException: Unresolved constraint in bundle org.eclipse.equinox.registry [4]: Unable to resolve 4.0: missing requirement [4.0] osgi.wiring.package; (osgi.wiring.package=org.eclipse.osgi.service.datalocation) [caused by: Unable to resolve 2.0: missing requirement [2.0] osgi.ee; (|(&(osgi.ee=JavaSE)(version=1.4.0))(&(osgi.ee=CDC/Foundation)(version=1.0.0))(&(osgi.ee=JavaSE)(version=1.3.0)))]
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4002) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2045) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304) [org.apache.felix.main.jar:na]
at java.base/java.lang.Thread.run(Thread.java:844) [na:na]
Error starting file:/usr/share/java/protege/bundles/protege-editor-core.jar
org.osgi.framework.BundleException: Unresolved constraint in bundle org.protege.editor.core.application [5]: Unable to resolve 5.0: missing requirement [5.0] osgi.wiring.package; (&(osgi.wiring.package=org.eclipse.core.runtime)(registry=split)(version>=3.4.0)(!(version>=4.0.0))) [caused by: Unable to resolve 4.0: missing requirement [4.0] osgi.wiring.package; (osgi.wiring.package=org.eclipse.osgi.service.datalocation) [caused by: Unable to resolve 2.0: missing requirement [2.0] osgi.ee; (|(&(osgi.ee=JavaSE)(version=1.4.0))(&(osgi.ee=CDC/Foundation)(version=1.0.0))(&(osgi.ee=JavaSE)(version=1.3.0)))]]
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4002) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2045) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304) [org.apache.felix.main.jar:na]
at java.base/java.lang.Thread.run(Thread.java:844) [na:na]
Error starting file:/usr/share/java/protege/bundles/logback-classic.jar
org.osgi.framework.BundleException: Unresolved constraint in bundle ch.qos.logback.classic [6]: Unable to resolve 6.0: missing requirement [6.0] osgi.wiring.package; (&(osgi.wiring.package=ch.qos.logback.core.util)(version>=1.1.0)(!(version>=2.0.0))) [caused by: Unable to resolve 13.0: missing requirement [13.0] osgi.ee; (&(osgi.ee=JavaSE)(version=1.6))]
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4002) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2045) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304) [org.apache.felix.main.jar:na]
at java.base/java.lang.Thread.run(Thread.java:844) [na:na]
Error starting file:/usr/share/java/protege/bundles/jul-to-slf4j.jar
org.osgi.framework.BundleException: Unresolved constraint in bundle jul.to.slf4j [8]: Unable to resolve 8.0: missing requirement [8.0] osgi.wiring.package; (&(osgi.wiring.package=org.slf4j)(version>=1.7.12)) [caused by: Unable to resolve 9.0: missing requirement [9.0] osgi.ee; (&(osgi.ee=JavaSE)(version=1.5.0))]
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4002) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2045) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304) [org.apache.felix.main.jar:na]
at java.base/java.lang.Thread.run(Thread.java:844) [na:na]
Error starting file:/usr/share/java/protege/bundles/slf4j-api.jar
org.osgi.framework.BundleException: Unresolved constraint in bundle slf4j.api [9]: Unable to resolve 9.0: missing requirement [9.0] osgi.ee; (&(osgi.ee=JavaSE)(version=1.5.0))
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4002) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2045) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304) [org.apache.felix.main.jar:na]
at java.base/java.lang.Thread.run(Thread.java:844) [na:na]
Error starting file:/usr/share/java/protege/bundles/guice.jar
org.osgi.framework.BundleException: Unresolved constraint in bundle com.google.inject [12]: Unable to resolve 12.0: missing requirement [12.0] osgi.ee; (&(osgi.ee=JavaSE)(version=1.6.0))
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4002) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2045) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304) [org.apache.felix.main.jar:na]
at java.base/java.lang.Thread.run(Thread.java:844) [na:na]
Error starting file:/usr/share/java/protege/bundles/logback-core.jar
org.osgi.framework.BundleException: Unresolved constraint in bundle ch.qos.logback.core [13]: Unable to resolve 13.0: missing requirement [13.0] osgi.ee; (&(osgi.ee=JavaSE)(version=1.6))
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4002) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2045) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304) [org.apache.felix.main.jar:na]
at java.base/java.lang.Thread.run(Thread.java:844) [na:na]
Error starting file:/usr/share/java/protege/bundles/owlapi-osgidistribution.jar
org.osgi.framework.BundleException: Unresolved constraint in bundle org.semanticweb.owl.owlapi [17]: Unable to resolve 17.0: missing requirement [17.0] osgi.wiring.package; (&(osgi.wiring.package=com.google.inject)(version>=1.4.0)(!(version>=2.0.0))) [caused by: Unable to resolve 12.0: missing requirement [12.0] osgi.ee; (&(osgi.ee=JavaSE)(version=1.6.0))]
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4002) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2045) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304) [org.apache.felix.main.jar:na]
at java.base/java.lang.Thread.run(Thread.java:844) [na:na]
Error starting file:/usr/share/java/protege/bundles/protege-editor-owl.jar
org.osgi.framework.BundleException: Unresolved constraint in bundle org.protege.editor.owl [19]: Unable to resolve 19.0: missing requirement [19.0] osgi.wiring.package; (&(osgi.wiring.package=org.eclipse.core.runtime)(registry=split)(version>=3.4.0)(!(version>=4.0.0))) [caused by: Unable to resolve 4.0: missing requirement [4.0] osgi.wiring.package; (osgi.wiring.package=org.eclipse.osgi.service.datalocation) [caused by: Unable to resolve 2.0: missing requirement [2.0] osgi.ee; (|(&(osgi.ee=JavaSE)(version=1.4.0))(&(osgi.ee=CDC/Foundation)(version=1.0.0))(&(osgi.ee=JavaSE)(version=1.3.0)))]]
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4002) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2045) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304) [org.apache.felix.main.jar:na]
at java.base/java.lang.Thread.run(Thread.java:844) [na:na]
Error starting file:/usr/share/java/protege/bundles/log4j-over-slf4j.jar
org.osgi.framework.BundleException: Unresolved constraint in bundle log4j.over.slf4j [20]: Unable to resolve 20.0: missing requirement [20.0] osgi.wiring.package; (&(osgi.wiring.package=org.slf4j)(version>=1.6.0)) [caused by: Unable to resolve 9.0: missing requirement [9.0] osgi.ee; (&(osgi.ee=JavaSE)(version=1.5.0))]
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4002) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2045) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304) [org.apache.felix.main.jar:na]
at java.base/java.lang.Thread.run(Thread.java:844) [na:na]
The OSGi framework has been started

-- Here is a comparison for the messages from the manually-installed downloaded version --

$ ./run.sh
CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot
********************************************************************************
** Protege **
********************************************************************************

----------------- Initialising and Starting the OSGi Framework -----------------
FrameworkFactory Class: org.apache.felix.framework.FrameworkFactory

The OSGi framework has been initialised
------------------------------- Starting Bundles -------------------------------
Starting bundle org.protege.common
Starting bundle org.eclipse.equinox.common
Starting bundle org.eclipse.equinox.supplement
Starting bundle org.eclipse.equinox.registry
Starting bundle org.protege.editor.core.application
Starting bundle org.apache.commons.io
Starting bundle com.google.guava
Starting bundle com.googlecode.javaewah.JavaEWAH
Starting bundle org.jsr-305
Starting bundle jul.to.slf4j
Starting bundle log4j.over.slf4j
Starting bundle ch.qos.logback.classic
Starting bundle ch.qos.logback.core
Starting bundle org.apache.servicemix.bundles.aopalliance
Starting bundle org.apache.servicemix.bundles.javax-inject
Starting bundle org.eclipse.equinox.common
Starting bundle org.eclipse.equinox.registry
Starting bundle org.eclipse.equinox.supplement
Starting bundle org.eclipse.jgit
Starting bundle org.semanticweb.owl.owlapi
Starting bundle org.protege.common
Starting bundle org.protege.editor.core.application
Starting bundle org.protege.editor.owl
Starting bundle slf4j.api
Starting bundle cellfie
Starting bundle code-generation
Starting bundle existentialquery
Starting bundle uk.ac.manchester.cs.owl.explanation
Starting bundle org.protege.ontograf
Starting bundle org.coode.dlquery
Starting bundle org.semanticweb.hermit
Starting bundle org.coode.browser
Starting bundle org.coode.owlviz
Starting bundle org.protege.owl.rdf
Starting bundle org.protege.editor.owl.rdf
Starting bundle swrltab-plugin
The OSGi framework has been started

------------------------------------ Protege -----------------------------------
Protege Desktop
Version 5.5.0, Build


----------------------------------- Platform -----------------------------------
Java: JVM 1.8.0_121-b13 Memory: 466M
Language: en, Country: CA
Framework: Apache Software Foundation (1.8)
OS: linux (4.20.17-1-MANJARO)
Processor: x86-64


------------------------------------ Plugins -----------------------------------
Plugin: Cellfie Protege 5.0+ Plugin (2.1.0)
Plugin: OWL Code Generation Plug-in (2.0.0)
Plugin: Existential Query (2.0.0)
Plugin: Explanation Workbench (3.0.0)
Plugin: OntoGraf (2.0.3)
Plugin: DL Query (4.0.1)
Plugin: HermiT Reasoner (1.4.3.456)
Plugin: Browser View (OWLDoc) (3.0.3)
Plugin: OWLViz (5.0.3)
Plugin: OWLAPI RDF Library (3.0.0)
Plugin: SPARQL Query Plugin (3.0.0)
Plugin: SWRLTab Protege 5.0+ Plugin (2.0.6)

Creating and setting up empty (default) editor kit
OWL API Version: 4.5.9.2019-02-01T07:24:44Z
### Excluding compile: javax.swing.text.GlyphView::getBreakSpot
Cannot generate ontology catalog for ontology at http://www.semanticweb.org/daviding/ontologies/2019/3/untitled-ontology-3. URI scheme is not "file"
------------------------------- Auto-update Check ------------------------------
Auto-update last performed: Sat Apr 13 11:42:48 EDT 2019
Auto-update has not been performed today. Running it.

------------------------------ Running Auto-update -----------------------------

--- Searching for plugins ---
Checking https://raw.githubusercontent.com/protegeproject/autoupdate/master/update-info/5.0.0/plugins.repository
Processing https://raw.githubusercontent.com/protegeproject/autoupdate/master/update-info/5.0.0/plugins.repository as a plugin registry
Checking https://raw.githubusercontent.com/protegeproject/cellfie-plugin/master/update-info/protege-5/update.properties
Checking https://raw.githubusercontent.com/co-ode-owl-plugins/change-tracker/master/update-info/protege-5/update.properties
Checking https://raw.githubusercontent.com/protegeproject/csv-export-plugin/master/src/main/resources/update.properties
Checking https://raw.githubusercontent.com/protegeproject/dlquery/master/update-info/protege-5/update.properties
Checking http://elk.semanticweb.org/maven/latest/elk-distribution/resources/p5.update.properties
Checking https://raw.githubusercontent.com/protegeproject/existentialquery/master/update-info/protege-5/update.properties
Checking https://bitbucket.org/dtsarkov/factplusplus/downloads/config.autoupdate.Protege-5.0.txt
Checking https://raw.githubusercontent.com/julianmendez/jcel/master/update-info/protege-5/update.properties
Checking http://www.obdasystems.com/sites/default/files/download/plug-in/update.properties
Checking https://raw.githubusercontent.com/co-ode-owl-plugins/matrix/master/etc/update.matrix.properties
Checking https://raw.githubusercontent.com/protegeproject/ontograf/master/update-info/protege-5/update.properties
Checking http://isbi.aau.at/ontodebug/update.properties
Checking https://kbss.felk.cvut.cz/tools/owlhierarchy/update.properties
Checking https://github.com/ontop/ontop/raw/master/ontop-protege/update.properties
Checking https://raw.githubusercontent.com/protegeproject/rdf-library/master/update-info/protege-5/update.properties
Checking https://raw.githubusercontent.com/protegeproject/owl-diff/master/update-info/protege-5/update.properties
Checking https://raw.githubusercontent.com/co-ode-owl-plugins/owldoc/master/update-info/protege-5/update.properties
Checking https://raw.githubusercontent.com/protegeproject/owlviz/master/update-info/protege-5/update.properties
Checking https://raw.githubusercontent.com/Complexible/pellet/master/protege/plugin/plugins.repository
Processing https://raw.githubusercontent.com/Complexible/pellet/master/protege/plugin/plugins.repository as a plugin registry
Checking https://raw.githubusercontent.com/Complexible/pellet/master/protege/plugin/update.properties
Checking https://raw.githubusercontent.com/protegeproject/autoupdate/master/snap-sparql-query/update-info/protege-5/update.properties
Checking https://raw.githubusercontent.com/KITE-Cloud/SRE/master/update.properties
Checking https://raw.githubusercontent.com/protegeproject/sparql-query-plugin/master/update-info/protege-5/update.properties
Checking https://raw.githubusercontent.com/protegeproject/swrltab-plugin/master/update-info/protege-5/update.properties
Checking https://raw.githubusercontent.com/md-k-sarker/OWLAx/master/update.properties
Checking https://raw.githubusercontent.com/md-k-sarker/ROWL/master/update.properties
Checking https://raw.githubusercontent.com/owlcollab/protege-obo-plugin/master/update.properties
Checking https://raw.githubusercontent.com/onor13/odase.protege.plugins.repository/master/odase.plugins.repository
Processing https://raw.githubusercontent.com/onor13/odase.protege.plugins.repository/master/odase.plugins.repository as a plugin registry
Checking https://raw.githubusercontent.com/onor13/odase.protege.plugin.propertiesInDomainClass/master/update.properties
Checking https://raw.githubusercontent.com/onor13/odase.protege.plugin.individualPropertiesContextualAssertions/master/update.properties
Checking https://raw.githubusercontent.com/NJITSABOC/oaf-protege/OAFSummarizationPlugin/update-info/protege-5/update.properties