I think you should be using the corresponding Arduino blocks instead of MATLAB functions. Please see if these downloads are of help:
Arduino.m file not working with Simulink
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I tried using a Matlab function block in simulink. In the Matlab function I make other function calls that use the Arduino.m file, downloaded from the support page ( http://www.mathworks.com/matlabcentral/fileexchange/32374). I get a bunch of errors related to the arduino.m file such as the destructor not being used for code generation and try-catch statements can't be used for code generation and so on. My code works fine when it's a standalone m-script (not encapulated in a simulink block). Does anyone know if there's a compatible arduino m file that works with simulink? Thank you.
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