Okay, so you're building an eglib-based image. That explains some of that. I haven't tried building that one so no idea. I guess something gots wrong with some of the dependencies the module builds, so it doesn't find these libraries, but on the uclibc-based image and on the supported host OS (OpenSUSE 12.3) it compiles just fine for me.
The ending part looks a bit different in your and my logs, though it doesn't provide too much insight into that. At this point I don't think I'd have any suggestions other than trying that on the supported OS (Ubuntu 12.04, Debian Wheezy, OpenSUSE 12.3) and running bitbake with "-D" switch to see some more debug output.
FWIW that's what I see in my log, around the place they start to differ (numbers are line numbers):
474 build_src: building npy-pkg config files
475 running build_py
476 copying numpy/version.py -> build/lib.linux-x86_64-2.7/numpy
477 copying build/src.linux-x86_64-2.7/numpy/__config__.py -> build/lib.linux-x86_64-2.7/numpy
478 copying build/src.linux-x86_64-2.7/numpy/distutils/__config__.py -> build/lib.linux-x86_64-2.7/numpy/distutils
479 running build_clib
480 customize UnixCCompiler
481 customize UnixCCompiler using build_clib
482 running build_ext
483 customize UnixCCompiler
484 customize UnixCCompiler using build_ext
485 running scons
486 running build_scripts
487 adding 'build/scripts.linux-x86_64-2.7/f2py' to scripts
488 DEBUG: Shell function do_compile finished
