WordPress functions.php does not affect the theme menus

Try with adding this code into header.php, where menu usually appears. In functions.php you can declare custom menus, but you are calling them in header.php or wherever you want menus to appear.

Function register_nav_menus() declares menus and should go into functions.php, while wp_nav_menu() outputs menus you declared anywhere on the page (so not inside functions.php).

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