Adam Stewart added the comment:

> I'm certainly not going to try to deeply analyze a build that inserts *that* 
> many separate -I and -L options into the compiler calls

I believe those were necessary to get the build working. Spack doesn't install 
anything into /usr/, and without those flags, Python doesn't know where to 
search for its dependencies. I tried removing them anyway but it didn't help.

> My guess is that you will find that the problem goes away if you avoid the 
> use of '--enable-shared' on the Python configure

Just tried this and it does indeed go away! I can try convincing the other 
developers that this is the best option.

> most Python distributions on macOS use --enable-framework rather than 
> --enable-shared and we seldom test it.

I just tried using using `--enable-framework` and `make install` failed. Seeing 
lots of `ImportError: No module named site` errors.

> You should also check that there are no third-party Python 2.7's on PATH 
> and/or Python 2.7 shared libraries on the dyld library search paths, other 
> than the Apple-supplied pythons in /usr/bin.

This could very well be the cause of the problem. I happen to have both Python 
2 and 3 installed with both Homebrew and Anaconda, and all 4 are in my PATH. I 
don't have any PYTHON or LD/DYLD related env vars though. If you think it's 
worth testing, I can try removing everything from my PATH except /usr/bin:/bin

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<http://bugs.python.org/issue29846>
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