That warning is normal and can be safely ignored. The problem is that they changed the recipes in Arduino IDE 1.6.6 but in order for the cores to be still compatible with previous IDE versions they can't use the new recipe but 1.6.6 automatically converts the old recipe format so it doesn't cause any problems. For some reason they decided we have to see this annoying warning constantly even when not compiling for one of those boards. Even worse is they used the new recipe format in Arduino AVR Boards 1.6.9 so if you install it on any IDE before 1.6.6 then nothing will compile.