Previous 1 2 3 Next 40 Replies Latest reply: Aug 23, 2013 12:22 PM by Tobit Go to original post
  • Sidney Markowitz - Biomatters Level 1 (0 points)

    Hi, I'm the developer at Biomatters who tracked this down for Geneious. Here is what I found.


    It has always been the case that the Swing documentation says that all Swing methods must be called only from within the Swing thread unless the method's API doc specifically says that method is thread-safe. Up to now there have been no problems seen calling some methods that do not say "thread-safe" in the javadoc and that seem like they don't cause actions in the GUI and should be safe. In particular, it is common to not think about threads when you initialize the Swing GUI layout theme by calling UIManager.setLookAndFeel() at the very start of running an application, before you display anything.


    With this update to Java 6 we have found that you must wrap the call to UIManager.setLookAndFeel to ensure it is called from within the Swing thread, just like you do with other Swing calls. Some small test programs that don't do that still seem to work, but you can no longer get away with it.


    It is probably common practice to set the application's look and feel when it starts up. If you do, change that to do it in the Swing (also known as the dispatch or the GUI) thread.


    There may be other Swing methods that are not documented as thread-safe which used to let you get away with that too, so check your use of Swing to ensure that you are properly using the methods that are not labeled in their JavaDoc as thread-safe.

  • GregoryL Level 1 (5 points)

    Java on Mac is an Apple "child". They decided to maintain it in house and disallowed SUN/Oracle (prior to Java 7) to do so. Java 6 is a part of OS X and supplied solely by Apple. So the fault is....

  • marchila Level 1 (0 points)
  • marchila Level 1 (0 points)


  • woodmeister50 Level 5 (5,170 points)

    I agree with some comments on here that Java is basically a mess

    in and of itself!


    Been forced to use Java based applications over the years and found

    more often then not, ANY Java update would break applications.  This

    has not been limited to just Mac platform, it happens on Windows and Linux

    machines as well!


    So, the ultimate fault lies in the miserable mess that is Java and its total

    lack of backward compatibility!

  • ggoemans Level 1 (0 points)

    I have the same problem, only difference is that I am running OS X 10.6.

    There is an update that fixes the OS X 10.7 Java update (, but as far as I can tell there isn't a update available (yet) for any earlier versions


    Geneious indeed has been great and very fast in coming up with an update that fixes the issues caused by yesterdays Java update.

  • hpp23 Level 1 (0 points)

    I have changed all my Java Swing Applications to make them run with the "Java for OS X 2013-004" update:


    This solves the GUI problems if you are able to edit and compile the Java source:


    Within the "main" class that contains:


    public static void main(String[] args) { ... }


    change this main function into


    private static void createAndShowGUI(String[] args) { ... }



    with main's function body.


    Now add a new main function, as follows:


    public static void main(final String[] args) {
        javax.swing.SwingUtilities.invokeLater(new Runnable() {
            public void run() {
  • Tobit Level 1 (15 points)

    For once, you're wrong ;-)


    If Apple's cache servers are still delivering the "M4508", use the following link to download the updated version (M4509): e_Software_Updates/Mac_OS_X/downloads/091-7278.20130621.Ts30t/JavaForOSX2013-004 .dmg



  • lmmeredith2 Level 1 (0 points)

    I was having trouble with a particular Java application before I installed the above Java update. It moved me from Java(TM) SE Runtime Environment (build 1.6.0_51-b11-457-11M4508) to Java(TM) SE Runtime Environment (build 1.6.0_51-b11-457-11M4509).


    The application works now, but I still get these error messages in


    7/28/13 2:20:50.484 PM JavaApplicationStub: CGContextGetCTM: invalid context 0x0

    7/28/13 2:20:50.484 PM JavaApplicationStub: CGContextSetBaseCTM: invalid context 0x0


    (and there are more of these ...).


    Does anyone know why?

  • jlkenney Level 1 (0 points)

    Hi Nixwizard,

    I was wondering if you are still having trouble with FigTree. Recent updates seem to have fixed all my phylogenetics stuff with geneious and dendoscope, but I recently tried to download FigTree and was unable to. I'm wondering if this is something other people are still seeing since the Java problem. Thanks!



  • Tobit Level 1 (15 points)

    Everything is fine with FigTree 1.4.0 and my up-to-date OSX... (daily used)



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