Arch Linux User Repository

cytoscape requires java-11-openjdk. If you experiences issues with cytoscape "using" the wrong java version, make sure the JAVA_HOME environment variable is NOT set. Though not necessary, you can also use the command archlinux-java to set your default java environment to java-11-openjdk (remember to restore it if you need another version for other applications)

archlinux-java set java-11-openjdk

See also my other comment

cytoscape requires java-11-openjdk. If you experiences issues with cytoscape "using" the wrong java version, make sure the JAVA_HOME environment variable is NOT set. Though not necessary, you can also use the command archlinux-java to set your default java environment to java-11-openjdk (remember to restore it if you need another version for other applications)

archlinux-java set java-11-openjdk

See also my other comment

Edit: forget my previous comment. I have edited my comment.

@vstuart: The problem is that you set JAVE_HOME to the wrong version of java. this requires java-11-openjdk. The solution is to run

export PATH=/usr/lib/jvm/java-11-openjdk/bin:"$PATH" && cytoscape 

or use the command archlinux-java to set the default java environment by running sudo archlinux-java java-11-openjdk.

This package uses the same package from upstream. The only difference is that is is installed globally instead of locally as I guess you did.

I very much appreciate the effort put into maintaining these packages. That said, the AUR version failed to load (output appended).

Therefore, I installed the latest Linux version (3.8.2) directly from https://cytoscape.org/download.html via their BASH script installer, which quickly installed a working version, accessible via the application shortcut that was automatically added to the Whiskers menu. Quick and painless.

The downloaded binary apparently includes / uses Java 11 (which is listed as a requirement on the download page: "Please install Java 11 before using Cytoscape").

In the new version (3.8.2): Help menu >> About >>

Version: 3.8.2
Java: 11.0.10 by Oracle Corporation
Java Home: /usr/lib/jvm/java-11-openjdk
OS: Linux 5.11.6-arch1-1 - amd64

## AUR-installed, non-working version:
[victoria@victoria ~]$ which cytoscape                                                                                                     
  /usr/bin/cytoscape

[victoria@victoria ~]$ cytoscape -v
  Cytoscape version: 3.8.2

[victoria@victoria cytoscape-3.8.2]$ java --version
  openjdk 15.0.2 2021-01-19
  OpenJDK Runtime Environment (build 15.0.2+7)
  OpenJDK 64-Bit Server VM (build 15.0.2+7, mixed mode)

[victoria@victoria ~]$ date
2021-03-26 15:48:48 -0700 (PST)

[victoria@victoria ~]$ cytoscape

karaf.base: /opt/cytoscape/framework

JAVA_HOME: /usr/lib/jvm/java-15-openjdk/

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:/opt/cytoscape/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

[victoria@victoria ~]$ 

JAVA_HOME out of the box not being set is annoying, but not having AA enabled makes this software nearly impossible to use.

The application command entry might benefit from being changed to reflect one or both improvements:

1 Depend on jdk8 and link it directly + turn on AA:

JAVA_HOME=/usr/lib/jvm/java-8-openjdk/ _JAVA_OPTIONS='-Dawt.useSystemAAFontSettings=on' cytoscape

2 Don't depend on jdk8 and turn on AA:

_JAVA_OPTIONS='-Dawt.useSystemAAFontSettings=on' cytoscape

I used #1 while working towards getting this running.

K

Current version bump to 3.8.2

I was playing with the PKGBUILD and updated it to version 3.8.2 by making the following changes

1. Changed pkgver
2. Updated the URL to match the new release naming scheme as of 3.8.2
3. Computed the sha256sum for the updated package and added it to the PKGBUILD

I have included a gist with the illustrated changes for your convenience. I'd be delighted to help co-maintain and test the package long term.

https://gist.github.com/evikv/cb2191582103e939bb3c78d8554144e5

FYI: I installed Cytoscape 3.8. with the official Linux installer from cytoscape.org. Java 8-openjdk did not work, but Java 11-openjdk does. I haven't tried Java 14-openjdk.

One more suggestion -- Cytoscape is not compatible with recent versions of Java so you first have to install an earlier version (JDK-8 is the one currently listed as supported), and then you should be able to launch cytoscape with "JAVA_HOME=/usr/lib/jvm/java-8-openjdk cytoscape"

Crash at startup

Error occurred during initialization of boot layer java.lang.module.FindException: Module java.transaction not found

https://github.com/cytoscape/cytoscape/releases/download/3.7.1/cytoscape-3.7.1.tar.gz

outdate