New Cytoscape 3.8.2 installation throws an error regarding installing bundles

[Nitish Narula]

Hello,

I just installed Cytoscape 3.8.2 on a multi-user Linux (RHEL7) server with Java 12. The installation went fine without error. However when I try to start Cytoscape (either with Cytoscape or cytoscape.sh) I get the following error. I am not able to parse this out. Has any one seen this error before and is there a workaround? Please let me know if I can provide more information. Thank you.

karaf.base: /usr/local/apps/Cytoscape/3.8.2/framework
JAVA_HOME: /usr/local/Java/jdk-12.0.1
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="4.2.4",org.apache.karaf.jaas.boot.principal;uses:=javax.security.auth;version="4.2.4",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="4.2.4",org.apache.karaf.info;version="4.2.4",,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:80)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.felix.framework.URLHandlers (file:/usr/local/apps/Cytoscape/3.8.2/framework/system/org/apache/felix/org.apache.felix.framework/5.6.12/org.apache.felix.framework-5.6.12.jar) to constructor sun.net.www.protocol.file.Handler()
WARNING: Please consider reporting this to the maintainers of org.apache.felix.framework.URLHandlers
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
Error installing bundle listed in startup.properties with url: mvn:org.apache.karaf.features/org.apache.karaf.features.extension/4.2.4 and startlevel: 1

[David Otasek]

It looks like you are using Java 12. Cytoscape 3.8+ requires a Java 11 VM to function. You can find an appropriate VM here: https://adoptopenjdk.net/

Once installed, you may need to set your JAVA_HOME to point to this VM. We have a guide for this here: https://cytoscape.org/common_issues.html#java_home

[Nitish Narula]

Thanks, David. I had misunderstood the documentation thinking anything above Java 11 would work. I have reinstalled Cytoscape with a localized Java 11 VM installation and everything seems to be working correctly.

Thanks again,

Nitish