Here's one piece of advice - most of the time spent by the MATLAB compiler is in the dependency check for the code you are compiling. If there are a large number of toolkits along the way, this can be time consuming. You can change the list of toolboxes on the way to the "Settings" menu in deploytool . Make sure that only the toolbars that your code uses are selected.
It may take ages, but it can lead to less age.
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