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I can confirm this behaviour under Ubuntu Jaunty. I found several similar bug reports when I Googled the error.

See On Jul 16, 7:33 am, Douglas Murray wrote: >Cytoscape does not install on Jaunty. >Details: >glitterbox:~/Desktop$ uname -a >Linux glitterbox 2.6.28-14-generic #46-Ubuntu SMP Wed Jul 8 07:41:18 >UTC 2009 x86_64 GNU/Linux >glitterbox:~/Desktop$ java -version >java version '1.6.0_14' >Java(TM) SE Runtime Environment (build 1.6.0_14-b08) >Java HotSpot(TM) 64-Bit Server VM (build 14.0-b16, mixed mode) >>glitterbox:~/Desktop$ sh Cytoscape_2_6_3_unix.sh >Puzzle Bobble Taito. Starting Installer.

Java SE 6 Update 14 Release Notes. For this update release is 1.6.0_14-b08 (where 'b' means 'build'). Error has been detected by Java Runtime Environment'.