compiling in build subdirectory does not work

I'm trying to build the library inside a subdirectory named "build" to leave the sources clean for subsequent builds but I am getting the following errors:

Creating include/BoardConfig.h...../configure: 242: ../configure: cannot create include/BoardConfig.h: Directory nonexistent

Then when trying to make:
make: *** No rule to make target 'src/Board.cpp', needed by 'obj/Board.o'.  Stop.