1. CommFinder does not appear under "plugins" tab.

    2. Make sure you installed the right version of Cytoscape (2.6.3). Also, if CommFinder was installed manually, make sure the jar file is placed under the plugins directory.

  2. I am trying to download MCR from the webpage but I am gettig "Error reading setup initialization file".

    3. Delete temporary files, refresh the webpage and try again..

  3. I am trying to run "MCRInstaller.bin" but I am getting permission denied error.

    4. Issue "chmod +x MCRInstaller.bin" command, then try to run it again.

  4. When trying to install MCR on linux, I get an error: usr/share/themes/Human/gtk-2.0.

    5. Disable the visual settings: System => Preference => Appearance => Visual Effects => None.

  5. I installed CommFinder from Cytoscape. When trying to install MCR from the link given on the plugin selection I do not see anything.

    6. Modify the default web browser setting on Cytoscape to your current web browser: Edit => Preferences => Properties => defaultWebBrowser

  6. I downloaded CommFinder from the webpage and saved it under plugins. When I open Cytoscape, I do not see it under plugins.

    7. The downloaded file might be corrupted. Try refreshing the browser and download again. The jar file size should be around 950 KB.

  7. When running QCUT from CommFinder, the window shows up and dissappears. When I try to run again, I get the message "result exist".

    8. Make sure you have the path set correctly as specified on the manual.

  8. I get the message "result exist" when I run the algorithm.

    9. Make sure the previous result of the algorithm is closed. You can export and save the previous result if needed.