Common Issue

Inability to install on Mac OS

If a Cytoscape installer for Mac (.dmg) fails to launch when double-clicked (e.g., trouble identifying developer), it is either an early release or awaiting an Apple developer signature.

SOLUTION: Right-click on the .dmg and choose "Open". This will give you the option to open the installer anyways.

Inability to start on Mac OS

Recent updates of Mac OS have caused the OpenCL based Cytoscape Apps to fail on some machines. If this is the case, you can disa ble OpenCL with the following method:

Download the disable-opencl.dummy file to your CytoscapeConfiguration directory. You can browse to this directory from the Home location on your Mac. After you have downloaded it, your folder should look similar to th e screenshot below.

Alternatively, if you are comfortable using terminals, you can create this file using the following command:touch ~/Cytosc apeConfiguration/disable-opencl.dummy

Troubleshooting

System Checker Script

Cytoscape is a Java application and it requires some third-party software packages to run properly. To test your system, please download the following script first.

How to Test Your System: Linux and Mac

Open Terminal

Go into download directory

This depends on where you saved the script above.

Make the script executable

You need to change permission to make it runnable. For Linux, change "mac.sh" to "linux.sh".

Test your system

After few seconds, it should desplay the test results. For Linux, change "mac.sh" to "linux.sh".

How to Test Your System: Windows

Open directory where you saved "windows.bat"

This is probably either "Downloads" or Desktop

Double click on "windows.bat" to test your system

After few seconds, it should desplay the test results.

If your system passes all tests, you are ready to use Cytoscape.

Still Have Problems?

How to Report Issues

If the checker shows your machine is ready, and still unable to run Cytoscape, it can be a bug. Please report them from:

Help → Report a bug...

Or, you can directly report it from Report a bug link on the navigation bar.

Ask Questions

If you get error message from system checker script, and cannot solve the issue by yourself, please search for your issue among Cytoscape-tagged Bioinformatics StackExchange posts or start a new post.

Cytoscape at Bioinformatics StackExchange

Known Issues

There are several known issues for this release. Please read the release notes to check those issues.

Release Notes: Known Issues

Don't forget to copy-and-paste outputs from the system checker script!

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