At times I am unable to clear classes in Matlab without restarting the program. This seems to be related to errors being thrown in the class. In other words, following an error I might make a change to the class and then call "clear classes" to reset everything. Also, since 95% of the time I am working with handle classes, this may be handle class related.
Some issues I have run across that I know are not currently the problem are: 1) storage of the class in a figure which is still open 2) the default value of a property being a class
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Object references can leak via userdata or appdata, callbacks, the variable editor etc. Try closing all figures - but probably close the variable editor first.
With handle classes I have taken to maintaing a list in the figure appdata area maintained by calling a common superclass method from the constructors, and adding a DeleteFcn callback that calls a static superclass method to delete any remaining valid handle objects when a figure closes. A bit of a pain but it seems to work.
Two related, but not duplicate, questions are
There was also a related question sometime in the past few months where it eventually seemed like the problem was a bug (the problem disappeared in some release) It involved two classes calling each other. I can no longer find the question (which isn't surprising give the search capabilities of Answers).
Based on your example with class_1 and class_2, I think the problem is related to the fact that you are creating handle objects which contain shared copies of themselves (the temp property is passed copies of obj itself in the constructor). I can't explain why the problem occurs only for N>2, however, it's easy to see that you create a chicken-and-egg situation when MATLAB tries to delete an object of class_1: before MATLAB can delete an object of class_1, it must first delete all the data in the properties that it contains. However, the properties of the class_1 object contain the object itself!
Is there any way you can settle for unshared copies of class_1 in temp?
I have the same problem in Matlab 2015b. 'clear classes' throws a warning. Any thoughts on this one?