Error when trying to compile Numba on MacOS Mojave 10.14.6

Hey there I’m trying to compile Numba in order to put in a patch for a memory leak but I’m getting stuck at compilation.

Here’s the error message I’m getting:
(numbaenv) Andrews-MacBook-Pro:numba lycurgus$ python setup.py build_ext --inplace

TBB disabled

Using OpenMP from: /Users/lycurgus/miniconda3/envs/numbaenv

/Users/lycurgus/miniconda3/envs/numbaenv/lib/python3.7/site-packages/setuptools/dist.py:458: UserWarning: Normalizing '0.54.0dev0+540.gd4d09f378' to '0.54.0.dev0+540.gd4d09f378'

warnings.warn(tmpl.format(**locals()))

running build_ext

building 'numba._helperlib' extension

Warning: Can't read registry to find the necessary compiler setting

Make sure that Python modules winreg, win32api or win32con are installed.

C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/lycurgus/miniconda3/envs/numbaenv/include -arch x86_64 -I/Users/lycurgus/miniconda3/envs/numbaenv/include -arch x86_64

compile options: '-I/Users/lycurgus/miniconda3/envs/numbaenv/lib/python3.7/site-packages/numpy/core/include -I/Users/lycurgus/miniconda3/envs/numbaenv/include/python3.7m -c'

gcc: numba/_helpermod.c

gcc: numba/cext/dictobject.c

gcc: numba/cext/listobject.c

gcc: numba/cext/utils.c

gcc -bundle -undefined dynamic_lookup -L/Users/lycurgus/miniconda3/envs/numbaenv/lib -arch x86_64 -L/Users/lycurgus/miniconda3/envs/numbaenv/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.9-x86_64-3.7/numba/_helpermod.o build/temp.macosx-10.9-x86_64-3.7/numba/cext/utils.o build/temp.macosx-10.9-x86_64-3.7/numba/cext/dictobject.o build/temp.macosx-10.9-x86_64-3.7/numba/cext/listobject.o -L/Users/lycurgus/miniconda3/envs/numbaenv/lib/python3.7/site-packages/numpy/core/lib -lnpymath -o /Users/lycurgus/development/numba/numba/_helperlib.cpython-37m-darwin.so -headerpad_max_install_names

ld: in /Users/lycurgus/miniconda3/envs/numbaenv/lib/python3.7/site-packages/numpy/core/lib/libnpymath.a(npy_math.o), could not parse object file /Users/lycurgus/miniconda3/envs/numbaenv/lib/python3.7/site-packages/numpy/core/lib/libnpymath.a(npy_math.o): 'Unknown attribute kind (61) (Producer: 'LLVM11.1.0' Reader: 'LLVM APPLE_1_1001.0.46.4_0')', using libLTO version 'LLVM version 10.0.1, (clang-1001.0.46.4)' for architecture x86_64

clang: **error:** linker command failed with exit code 1 (use -v to see invocation)

error: Command "gcc -bundle -undefined dynamic_lookup -L/Users/lycurgus/miniconda3/envs/numbaenv/lib -arch x86_64 -L/Users/lycurgus/miniconda3/envs/numbaenv/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.9-x86_64-3.7/numba/_helpermod.o build/temp.macosx-10.9-x86_64-3.7/numba/cext/utils.o build/temp.macosx-10.9-x86_64-3.7/numba/cext/dictobject.o build/temp.macosx-10.9-x86_64-3.7/numba/cext/listobject.o -L/Users/lycurgus/miniconda3/envs/numbaenv/lib/python3.7/site-packages/numpy/core/lib -lnpymath -o /Users/lycurgus/development/numba/numba/_helperlib.cpython-37m-darwin.so -headerpad_max_install_names" failed with exit status 1

Any ideas what may be causing it?

Is this using the system compiler? IIRC there were some issues with that recently. Also, where did you get your Python from?

An idea might be to use the conda based compilers as outlined here:

https://numba.readthedocs.io/en/stable/user/installing.html