First of all thank you for the reply, I tried what you suggested and by going in the mentioned folder and running the command:

ninja

I get the same output message unfortunately:
ninja: error: '/home/michele/Documents/GitHub/MicheleDelliVeneri/Thesis/Code/nms_3D/nms_kernel.cu', needed by '/home/michele/Documents/GitHub/MicheleDelliVeneri/Thesis/Code/nms_3D/build/temp.linux-x86_64-3.8/nms_kernel.o', missing and no known rule to make it


am I misunderstanding what you meant by manually run ninja?