How to assign GPIO to pins I have assigned on DEO nano

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Generally no. As you project goes you'll get thousands of warnings, usually difficult to control, except if you use the supress function.

Which warning is it? Is it the one talking about the requirements for 2.5/3.0/3.3V banks? If yes it just means you need to be careful about voltage overshoot, as there is a close limit on what the FPGA can tolerate. (4.1V IIRC)