CODEWITHSUNDEEP
cytoscape
Thomson_123
Thomson_123

Reputation: 3

Issues with CytoScape - 3.10.0 - Not Launching - error installing bundle listed in startup.properties with url:

Looking for some advice, seeing an issue with Cytoscape version 3.10.0 not launching on Windows 10, running Adoptium jdk-11 , but have also tried jdk-17.0.8+7

In the Cytoscape output file I have the following error Error installing bundle listed in startup.properties with url: mvn:org.apache.karaf.features/org.apache.karaf.features.core/4.3.7 and startlevel: 15

I have tried other versions of the adoptium java environments, also tried the test from cytoscape that gets the following output :

Cytoscape test: 'jvmVariant' is not recognized as an internal or external command, operable program or batch file.

Cytoscape System Requirements Checker for Windows

Target Cytoscape version: 3.9.0

Your Windows version is:

Microsoft Windows [Version 10.0.19044.3086]

Java is installed

More details on Java

openjdk version "11.0.20" 2023-07-18 OpenJDK Runtime Environment Temurin-11.0.20+8 (build 11.0.20+8) OpenJDK 64-Bit Server VM Temurin-11.0.20+8 (build 11.0.20+8, mixed mode)

Your system is 64 bit

Your JAVA_HOME is set to C:\Program Files\Eclipse Adoptium\jre-11.0.20.8-hotspot\bin

Your Java Major version is 11 Your Java version is at least version 11 as required

Your Java version is no higher than version 11 as required

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 50642 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0

The "app" store at https://apps.cytoscape.org is reachable

Summary

Success! You are ready to run Cytoscape 3.9.0

Press any key to continue . . .

Upvotes: 0

Views: 292

Answers (1)

Scooter Morris
Scooter Morris

Reputation: 1388

Yes, we are aware of this issue. The latest versions of Java 11 and Java 17 introduced a breaking change that breaks zip files. There are two workarounds:

  1. Downgrade to Java 17.0.7 (the change was introduced in 17.0.8)
  2. Do export EXTRA_JAVA_OPTS="-Djdk.util.zip.disableZip64ExtraFieldValidation=true" before launching.

#2 would be very difficult in a Windows environment (you would need to edit the .bat file and only launch from that). I would recommend doing #1. We are working on a fix and will release a new version (3.10.1) shortly.

Upvotes: 0

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