Re: Error Launching Cytoscape Desktop 3.9.1 from Command Line (Cannot Install karaf.features)

[Christopher Churas]

Hi,

From the log it looks like your JAVA_HOME is set to Java 19. 

Cytoscape 3.9.1 only works with Java 11 JDK. 

To run cytoscape.bat on the commandline you'll need to set JAVA_HOME to a Java 11 installation. 

You could dig around and find the java 11 installed with Cytoscape (installed by install4j) or you could install this JDK:

https://adoptium.net/temurin/releases/?version=11

and set your JAVA_HOME environment before you invoke cytoscape.bat.

For the upcoming Cytoscape 3.10, we have made changes to cytoscape.bat to automatically try to find the correct 

version of Java installed by Cytoscape.

hope this helps,

chjris

On Fri, Mar 3, 2023 at 6:14 AM Kyle Higgins <higginsk...@gmail.com> wrote:

Hello,

I am having difficulty launching Cytoscape Desktop on Windows command line (and therefore debug mode for app development). What is odd is running as an application works just fine. When I try from command line I get the following error:

 

C:\Program Files\Cytoscape_v3.9.1>cytoscape.bat
karaf.base: C:\Program Files\Cytoscape_v3.9.1\framework\bin\..
JAVA_HOME: C:\Program Files\Java\jdk-19
ERROR: Error parsing system bundle export statement: org.osgi.dto;version="1.0",org.osgi.resource;version="1.0",org.osgi.resource.dto;version="1.0";uses:="org.osgi.dto",org.osgi.framework;version="1.8",org.osgi.framework.dto;version="1.8";uses:="org.osgi.dto",org.osgi.framework.hooks.bundle;version="1.1";uses:="org.osgi.framework",org.osgi.framework.hooks.resolver;version="1.0";uses:="org.osgi.framework.wiring",org.osgi.framework.hooks.service;version="1.1";uses:="org.osgi.framework",org.osgi.framework.hooks.weaving;version="1.1";uses:="org.osgi.framework.wiring",org.osgi.framework.launch;version="1.2";uses:="org.osgi.framework",org.osgi.framework.namespace;version="1.1";uses:="org.osgi.resource",org.osgi.framework.startlevel;version="1.0";uses:="org.osgi.framework",org.osgi.framework.startlevel.dto;version="1.0";uses:="org.osgi.dto",org.osgi.framework.wiring;version="1.2";uses:="org.osgi.framework,org.osgi.resource",org.osgi.framework.wiring.dto;version="1.2";uses:="org.osgi.dto,org.osgi.resource.dto",org.osgi.service.condpermadmin;version="1.1.1";uses:="org.osgi.framework,org.osgi.service.permissionadmin",org.osgi.service.packageadmin;version="1.2";uses:="org.osgi.framework",org.osgi.service.permissionadmin;version="1.2",org.osgi.service.resolver;version="1.0";uses:="org.osgi.resource",org.osgi.service.startlevel;version="1.1";uses:="org.osgi.framework",org.osgi.service.url;version="1.0",org.osgi.util.tracker;version="1.5.1";uses:="org.osgi.framework",org.apache.karaf.version;version="4.2.8",org.apache.karaf.jaas.boot.principal;uses:=javax.security.auth;version="4.2.8",org.apache.karaf.jaas.boot;uses:="javax.security.auth,javax.security.auth.callback,javax.security.auth.login,javax.security.auth.spi,org.osgi.framework";version="4.2.8",org.apache.karaf.info;version="4.2.8",,org.apache.karaf.branding, org.apache.html.dom; version="2.11.0", org.apache.wml.dom; version="2.11.0", org.apache.wml; version="2.11.0", org.apache.xerces.parsers; version="2.11.0", org.apache.xerces.impl.dtd.models; version="2.11.0", org.apache.xerces.xni.parser; version="2.11.0", org.apache.xerces.impl.dv.xs; version="2.11.0", org.apache.xerces.impl.xs.traversers; version="2.11.0", org.apache.xerces.util; version="2.11.0", org.apache.xerces.impl.dtd; version="2.11.0", org.apache.xerces.jaxp.validation; version="2.11.0", org.apache.xerces.dom3.as; version="2.11.0", org.apache.xerces.impl.dv; version="2.11.0", org.apache.xerces.jaxp; version="2.11.0", org.apache.xerces.jaxp.datatype; version="2.11.0", org.apache.xerces.impl.xpath.regex; version="2.11.0", org.apache.xerces.xni; version="2.11.0", org.apache.xerces.impl.msg; version="2.11.0", org.apache.xerces.impl.dv.util; version="2.11.0", org.apache.xerces.impl.xs.util; version="2.11.0", org.apache.xerces.dom; version="2.11.0", org.apache.xerces.dom.events; version="2.11.0", org.apache.xerces.impl.xs.opti; version="2.11.0", org.apache.xerces.impl; version="2.11.0", org.apache.xerces.xs; version="2.11.0", org.apache.xerces.impl.io; version="2.11.0", org.apache.xerces.xpointer; version="2.11.0", org.apache.xerces.impl.dv.dtd; version="2.11.0", org.apache.xerces.xinclude; version="2.11.0", org.apache.xerces.impl.xpath; version="2.11.0", org.apache.xerces.xs.datatypes; version="2.11.0", org.apache.xerces.impl.xs.identity; version="2.11.0", org.apache.xerces.impl.xs.models; version="2.11.0", org.apache.xerces.xni.grammars; version="2.11.0", org.apache.xerces.impl.xs; version="2.11.0", org.apache.xerces.impl.validation; version="2.11.0", org.apache.xml.serialize; version="2.11.0", sun.misc, org.cytoscape.launcher.internal, com.sun.xml.internal.bind, com.apple.eawt, javafx.collections.transformation, javafx.print, netscape.javascript
org.osgi.framework.BundleException: Exported package names cannot be zero length.
        at org.apache.felix.framework.util.manifestparser.ManifestParser.normalizeExportClauses(ManifestParser.java:876)
        at org.apache.felix.framework.util.manifestparser.ManifestParser.<init>(ManifestParser.java:215)
        at org.apache.felix.framework.ExtensionManager.<init>(ExtensionManager.java:261)
        at org.apache.felix.framework.Felix.<init>(Felix.java:429)
        at org.apache.felix.framework.FrameworkFactory.newFramework(FrameworkFactory.java:28)
        at org.apache.karaf.main.Main.launch(Main.java:256)
        at org.apache.karaf.main.Main.main(Main.java:178)
        at org.cytoscape.launcher.internal.Launcher.main(Launcher.java:74)
Error installing bundle listed in startup.properties with url: mvn:org.apache.karaf.features/org.apache.karaf.features.extension/4.2.8 and startlevel: 1

I have tried updating the karaf.features extension version in startup.properties, or eliminating it, both of which break the ability to startup even as an app. 

Could anyone advise me in troubleshooting this?

Thank you,
Kyle

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