Fix compile on Mac OS 10.14 with Python 3.6. See https://github.com/…

[histed]

…pandas-dev/pandas/issues/23424

Caiman master doesn't compile with a fresh Anaconda Python 3.6 install, throwing this error at the link step.

g++ -bundle -undefined dynamic_lookup -L/Users/histed/anaconda3/envs/caiman36/lib -arch x86_64 -L/Users/histed/anaconda3/envs/caiman36/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf/oasis.o -o build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf/oasis.cpython-36m-darwin.so
clang: warning: libstdc++ is deprecated; move to libc++ with a minimum deployment target of OS X 10.9 [-Wdeprecated]
ld: library not found for -lstdc++
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'g++' failed with exit status 1

The fix is to pass the -stdlib=libc++ to the linker as in attached pull req.

Pandas bug here: pandas-dev/pandas#23424 suggests that -mmacosx-version-min=10.9 is also required, but it didn't seem to be needed for me. On the other hand it doesn't seem to cause problems.

[histed]

also: the compile works even without this patch with Anaconda 3.7 install.
Thanks! Mark

[epnev]

@histed Thanks for this. Can you remove the oasis.cpp file from your PR (or re-submit a new one without it)? As far as I understand this file is being generated during compiling. Or is there a reason you included it?

[pgunn]

@histed I believe (not 100% sure) that the issue you saw is mentioned in the readme under known issues. Could you give the solution in there a go (if you have not done so yet)?

[histed]

@pgunn:

• removed auto-gen Cython file
• If you mean the 'xcode-select' steps in the README.md, these don't solve it. Those two lines are required, but they install clang/g++ from Xcode, and make sure the development headers are installed. I believe the present issue is due to linking with libstdc++.

[pgunn]

What's this # not needed part? Seems superfluous to our needs?

[histed]

per the pandas/numpy issue it should be needed, but appears not to be in my testing.

[pgunn]

@pgunn:

• removed auto-gen Cython file
• If you mean the 'xcode-select' steps in the README.md, these don't solve it. Those two lines are required, but they install clang/g++ from Xcode, and make sure the development headers are installed. I believe the present issue is due to linking with libstdc++.

Interesting - we had this tested, but maybe something changed again in upstream packages.