Compiling MATLAB code: Works in MATLAB but not when compiled

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I have a program that works when run using MATLAB, but when I compile it and execute it, I get to a certain point where it doesn't output anything. It just stops responding. It is using 1/4 of the CPU at this time, but it is not outputting any errors into the command line. I have MCR installed for my specific type of matlab (using 32-bit 2013a, compiling with 32-bit 2013a). Is there something else I am supposed to install with MCR? Like a runtime library?

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Image Analyst
Image Analyst 2014-5-6
编辑:Image Analyst 2014-5-6
And try throwing in some fprintf's in there so you can track what part of the code it's executing.

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