Common Issues

Here are some common problems encountered while running Cytoscape, and with instructions on how to solve them.

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 disable 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 the screenshot below.



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


Basic Troubleshooting

First, follow the steps outlined in our Troubleshooting page

If you’ve run the System Checker script on that page, please include the output from it in any bug reports or help requests. It will contain important information about your configuration that can help diagnose the problem.

Finding Additional Log Info

Sometimes, additional log info can be needed to diagnose Cytoscape problems. There are two sources of log information that can be further analyzed.

Console Output

This is console output from running Cytoscape. You will need to open a terminal in your operating system and copy any output you see produced.

Framework Log

This is a log file generated automatically by running Cytoscape. It is normally located in the following places.

Setting JAVA_HOME

Windows

Using Windows Settings
  1. Locate your Java installation directory

    If you didn't change the path during installation, it'll be something like C:\Program Files\Java\jdk1.8.0_65

    You can also type where java at the command prompt.

  2. Do one of the following:

    • Windows 7 Right click My Computer and select Properties > Advanced
    • Windows 8 Go to Control Panel > System > Advanced System Settings
    • Windows 10 Search for Environment Variables then select Edit the system environment variables
  3. Click the Environment Variables button.
  4. Under System Variables, click New.
  5. In the Variable Name field, enter JAVA_HOME
  6. In the Variable Value field, enter your JDK or JRE installation path.

    Example: C:\Progra~1\Java\adoptopenjdk-11-hotspot-amd64*

    *Note for Windows users on 64-bit systems:

    • Progra~1 = 'Program Files'
    • Progra~2 = 'Program Files(x86)'

  7. Click OK and Apply Changes as prompted

You'll need to close and re-open any command windows that were open before you made these changes, as there's no way to reload environment variables from an active command prompt. If the changes don't take effect after reopening the command window, restart Windows.

Using Windows Command Line

If you would prefer to set the JAVA_HOME (or JRE_HOME) variable via the command line:

  1. Open Command Prompt (make sure you Run as administrator so you're able to add a system environment variable).
  2. Set the value of the environment variable to your JDK (or JRE) installation path as follows:

    setx -m JAVA_HOME "C:\Progra~1\Java\jdk1.8.0_XX"

    If the path contains spaces, use the shortened path name.

  3. Restart Command Prompt to reload the environment variables then use the following command to check the it's been added correctly.

    echo %JAVA_HOME%

    You should see the path to your JDK (or JRE) installation.

Mac or Linux

  1. Open Terminal
  2. Confirm you have JDK by typing which java. It should show something like /usr/bin/java.
  3. Check you have the needed version of Java, by typing java -version.
  4. JAVA_HOME is essentially the full path of the directory that contains a sub-directory bin, which contains the JVM. It generally looks like this: /Library/Java/Home

    Set JAVA_HOME to this path using this command: export JAVA_HOME=/Library/Java/Home

  5. Use echo $JAVA_HOME to confirm the path
  6. You should now be able to run your application

This only sets JAVA_HOME for the current session. To persistently set it, follow these steps:

  1. Open Terminal
  2. Type emacs .profile to edit your profile.
  3. Add this to the end of the .profile file:

    JAVA_HOME=/Library/Java/Home
    export JAVA_HOME;

  4. Save and exit emacs; use the following key combinations and follow any prompts: ctrl-x, ctrl-s; ctrl-x, ctrl-c
  5. Open a new Terminal window and type: $JAVA_HOME/bin/java -version

    You should see something like the following:

    openjdk version "11.0.9" 2020-10-20
    OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.9+11)
    OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.9+11, mixed mode)

Scaling Cytoscape on a High DPI Monitor

Cytoscape may not scale well on High DPI monitors. If this is the case and you are running on a Linux machine, you can add the following line to the cytoscape.sh file:

export GDK_SCALE=2

This works on Ubuntu 18.04 with GNOME/Cinnamon. However, scaling is not respected if one starts the application via the Cytoscape.desktop application shortcut, only if launched from the terminal.