The difference is that Android have its own makefile format, and system libraries implementation. Instead of tools like gcc, g++, ld, gdb... android uses predefined scripts. Debugging requires starting gdbserver on emulator or device. Building native application on android creates two executable files, one stripped to the bones, without any debugging information regardless of a compiler debug flag (placed in /system/bin on target platform), and another which will contain debug information, and is placed in symbols directory on the host platform. When debugging, you need to debug the second one. Project properties should include location of android source code tree, and selected toolchain.