Just as it says, showWindow isn't defined on the PreferenceController class. In C++, this would be an error because it's statically typed and would say "method not defined", but since Objective-C is more flexible, this is only a warning. Without seeing the code, it's hard to tell what your mistake is though.
The warnings mean the object in question doesn't (as far as the compiler knows) implement those two methods. This means either your window controller is not inheriting from the right superclass, or the pointer to the window controller is of the wrong type. It may or may not be the reason your window isn't opening, it's impossible to tell from the warnings alone.
edit: from your full code it looks like you're declaring your controller as inheriting from NSObject, instead of NSWindowController.