Cytoscape crashes when importing a network with Cy3D as renderer

Whenever I import a Cy3D network in cytoscape, the program crashes. It does not show me any errors, just quits.

The file I import is *.gml format and here is some sample data:

graph [
  node [
    id 0
    label "172.18.64.0/24"
  ]
  node [
    id 1
    label "172.18.160.0/20"
  ]
  edge [
    source 0
    target 92
  ]
  edge [
    source 1
    target 188
  ]

I use Ubuntu 20.04.1 LTS and java.

Cytoscape version 3.8.2 and Cy3D version 1.1.3

olof@olof-ubuntu:~$ java -version
openjdk version "1.8.0_275"
OpenJDK Runtime Environment (build 1.8.0_275-8u275-b01-0ubuntu1~20.04-b01)
OpenJDK 64-Bit Server VM (build 25.275-b01, mixed mode)
olof@olof-ubuntu:~$ cat /etc/os-release 
NAME="Ubuntu"
VERSION="20.04.1 LTS (Focal Fossa)"

I recorded a quick video and put it on youtube to show what I mean.

cy3d ubuntu cytoscape crash

• 1,839 views • link

updated 5.6 years ago by scooter

• written 5.6 years ago by lundgrenolof •

1 answer

Greetings, Well, the first problem is that Cytoscape 3.8 requires Java 11. Can you try upgrading to OpenJDK 11 and try again?

-- scooter

• 0 views • link

written 5.6 years ago by scooter

@scooter, the same thing happens when I use java 11.

olof@olof-ubuntu:~$ java -version
openjdk version "11.0.10" 2021-01-19
OpenJDK Runtime Environment (build 11.0.10+9-Ubuntu-0ubuntu1.20.04)
OpenJDK 64-Bit Server VM (build 11.0.10+9-Ubuntu-0ubuntu1.20.04, mixed mode, sharing)

• 0 views • link

written 5.4 years ago by lundgrenolof •