As Jan pointed out, this issue doesn't necessarily look like something that is being caused due to MATLAB Runtime, unless you are trying to run this code outside of MATLAB, as a standalone application. Therefore, I am writing this answer assuming that you have built a standalone application and are facing issues. Be advised that path management works differently in deployed standalone applications, hence, something that works in MATLAB using relative paths might not work in a standalone application. If possible, make sure you are using complete/absolute/full paths, as opposed to relative paths. You can view the following article to understand path management in deployed applications: Path Management
The fact that you are receiving a licensing error might also be occurring if you do not have a MATLAB Compiler license.
However, if you are building a standalone, please post a detailed description of the issue, and sample code if possible.
Hope this helps!