Currently this warning is reported, which in turn is an error with errors as warnings:
/home/nolden/prj/llvm/ep/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: error:
"Using deprecated NumPy API, disable it by "
"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Werror,-W#warnings]
If you insert
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
in mitkPythonService.cpp before the NumPy include, you can see the errors.