pip install lws failed on Mac OSx Mojave fatal error: 'complex' file not found #include <complex>

Question

pip install lws failed on Mac OSx Mojave fatal error: 'complex' file not found #include <complex>

prathmesh36 opened this issue 6 years ago · comments

Prathmesh Mhapsekar commented 6 years ago

pip install lws
Collecting lws
Using cached https://files.pythonhosted.org/packages/3a/c7/856af2e1202e7a4c5102406196aa661edb402256e7ce2334be0c0d8afa2e/lws-1.2.tar.gz
Building wheels for collected packages: lws
Running setup.py bdist_wheel for lws ... error
Complete output from command /anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/wz/ynmzx_6s1yq9dt5gxd2qvpxm0000gn/T/pip-install-cj8ou7i7/lws/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /private/var/folders/wz/ynmzx_6s1yq9dt5gxd2qvpxm0000gn/T/pip-wheel-z65xwyrs --python-tag cp36:
running bdist_wheel
running build
running build_ext
building 'lws' extension
creating build
creating build/temp.macosx-10.7-x86_64-3.6
creating build/temp.macosx-10.7-x86_64-3.6/lwslib
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/include -arch x86_64 -I/anaconda3/include -arch x86_64 -Ilwslib/ -I/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/include/python3.6m -c lws.bycython.cpp -o build/temp.macosx-10.7-x86_64-3.6/lws.bycython.o -O3
warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
In file included from lws.bycython.cpp:252:
In file included from /anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821:
/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by "
^
lws.bycython.cpp:471:14: fatal error: 'complex' file not found
#include
^~~~~~~~~
2 warnings and 1 error generated.
error: command 'gcc' failed with exit status 1

Failed building wheel for lws
Running setup.py clean for lws
Failed to build lws
Installing collected packages: lws
Running setup.py install for lws ... error
Complete output from command /anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/wz/ynmzx_6s1yq9dt5gxd2qvpxm0000gn/T/pip-install-cj8ou7i7/lws/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/var/folders/wz/ynmzx_6s1yq9dt5gxd2qvpxm0000gn/T/pip-record-1426losf/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_ext
building 'lws' extension
creating build
creating build/temp.macosx-10.7-x86_64-3.6
creating build/temp.macosx-10.7-x86_64-3.6/lwslib
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/include -arch x86_64 -I/anaconda3/include -arch x86_64 -Ilwslib/ -I/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/include/python3.6m -c lws.bycython.cpp -o build/temp.macosx-10.7-x86_64-3.6/lws.bycython.o -O3
warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
In file included from lws.bycython.cpp:252:
In file included from /anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821:
/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by "
^
lws.bycython.cpp:471:14: fatal error: 'complex' file not found
#include
^~~~~~~~~
2 warnings and 1 error generated.
error: command 'gcc' failed with exit status 1

----------------------------------------

Command "/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/wz/ynmzx_6s1yq9dt5gxd2qvpxm0000gn/T/pip-install-cj8ou7i7/lws/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/var/folders/wz/ynmzx_6s1yq9dt5gxd2qvpxm0000gn/T/pip-record-1426losf/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/wz/ynmzx_6s1yq9dt5gxd2qvpxm0000gn/T/pip-install-cj8ou7i7/lws/

Jonathan Le Roux · Answer 1 · Sun Jan 20 2019 21:03:49 GMT+0800 (China Standard Time)

According to this thread, the fix is to install the latest updates for Xcode. Let me know if that works.

Prathmesh Mhapsekar · Answer 2 · Sun Jan 20 2019 23:04:52 GMT+0800 (China Standard Time)

Thank you, it worked after installing the XCode Command line tool Nov 2, 2018 update available on this link - https://developer.apple.com/download/more/

Ryan Butler · Answer 3 · Wed Jun 26 2019 07:32:27 GMT+0800 (China Standard Time)

This is failing for me too. I have tried with all the following versions:

11.0.0.0.1.1560537986 (Xcode 11 Beta 2)
10.2.1.0.1.1554506761 (macOS 10.14, Xcode 10.2.1)
10.2.0.0.1.1552586384 (macOS 10.14, Xcode 10.2)
10.1.0.0.1.1539992718 (macOS 10.14, Xcode 10.1)

I am using python version 3.7, with anaconda. The error message is as follows:

gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ryan.butler/.anaconda3/envs/Proteus/include -arch x86_64 -I/Users/ryan.butler/.anaconda3/envs/Proteus/include -arch x86_64 -Ilwslib/ -I/Users/ryan.butler/.anaconda3/envs/Proteus/lib/python3.7/site-packages/numpy/core/include -I/Users/ryan.butler/.anaconda3/envs/Proteus/include/python3.7m -c lws.cpp -o build/temp.macosx-10.7-x86_64-3.7/lws.o -O3
warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
In file included from lws.cpp:608:
In file included from /Users/ryan.butler/.anaconda3/envs/Proteus/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/ryan.butler/.anaconda3/envs/Proteus/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/ryan.butler/.anaconda3/envs/Proteus/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:
/Users/ryan.butler/.anaconda3/envs/Proteus/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
lws.cpp:828:14: fatal error: 'complex' file not found
    #include <complex>
             ^~~~~~~~~
2 warnings and 1 error generated.
error: command 'gcc' failed with exit status 1
make: *** [build] Error 1

Ryan Butler · Answer 4 · Wed Jun 26 2019 08:09:21 GMT+0800 (China Standard Time)

I'm 99% sure that this was related to this issue: pandas-dev/pandas#23424. At the very least, following the advice there fixed it for me! Basically, XCode 10 made the switch from libstdc++ to libc++, and because of some crazy shit here that is dependent on how you installed distutils, as well as whether you used to have older versions of Xcode installed, you may or may not have this bug.

To fix the bug, do the following (on Mac only!):
I had to modify setup.py:41 to add some compile and link arguments, specifically the -stdlib=libc++ argument. It should look something like this if you want to fix it on macOS:

ext_modules = [Extension("lws",
                             sources=[lws_module_src,"lwslib/lwslib.cpp"],
                             include_dirs=["lwslib/",np.get_include()],
                             language="c++",
                             extra_compile_args=["-O3", "-stdlib=libc++"],
                             extra_link_args=["-stdlib=libc++"])],

@Jonathan-LeRoux Perhaps this could be incorporated into the codebase, with some sort of check for OS? It appears as though a better/more comprehensive solution to the hotfix I have posted above is outlined in this PR: pandas-dev/pandas#24274

Jonathan Le Roux · Answer 5 · Fri Jul 05 2019 12:37:04 GMT+0800 (China Standard Time)

Thanks for the detailed analysis and the proposed fix.
I'm happy to incorporate some fix in the codebase. It seems to me that the strategy in the pandas PR pandas-dev/pandas#24274 is less likely to lead to errors on other platforms.
Did you confirm it worked on your system? I won't have a Mac available to try this out for several weeks.

Jonathan Le Roux · Answer 6 · Fri Jul 05 2019 14:53:56 GMT+0800 (China Standard Time)

I pushed an updated version to Github, but I'm having issues with posting to PyPI.
twine is complaining that my README is not formatted properly, but for some reason its checking tool is converting all text to lowercase, which breaks some links that are fine otherwise...

Jonathan Le Roux · Answer 7 · Fri Jul 05 2019 15:44:00 GMT+0800 (China Standard Time)

I think there is a bug in twine when checking rst files, so I moved the README to markdown.
1.2.1 is now up on PyPI, please check.

Ryan Butler · Answer 8 · Sat Jul 06 2019 00:24:18 GMT+0800 (China Standard Time)

OK, Ill check on this once I get access again to my macbook

Ryan Butler · Answer 9 · Tue Jul 09 2019 01:02:21 GMT+0800 (China Standard Time)

Yep it works! Thanks for the rapid response :)

Takuya Matsuda · Answer 10 · Sun Nov 17 2019 19:12:01 GMT+0800 (China Standard Time)

@TheButlah Your solution helped me, thank you very much.
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