Arch Linux User Repository

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