Cannot install POT on Mac with 'pip install POT'

[Linwei-Chen]

system: MacOS 10.15.1
pip install POT
Looking in indexes: http://mirrors.aliyun.com/pypi/simple/
Collecting POT
Downloading http://mirrors.aliyun.com/pypi/packages/4e/23/8aba82a55d40ac8c5f4313c1c51804dcb239ee3761b9789db1b621e43c87/POT-0.6.0.tar.gz (794kB)
|████████████████████████████████| 798kB 393kB/s
Requirement already satisfied: numpy in /Users/chenlinwei/anaconda3/envs/DL3.7/lib/python3.7/site-packages (from POT) (1.18.0)
Requirement already satisfied: scipy in /Users/chenlinwei/anaconda3/envs/DL3.7/lib/python3.7/site-packages (from POT) (1.1.0)
Requirement already satisfied: cython in /Users/chenlinwei/anaconda3/envs/DL3.7/lib/python3.7/site-packages (from POT) (0.29.2)
Building wheels for collected packages: POT
Building wheel for POT (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Users/chenlinwei/anaconda3/envs/DL3.7/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/tmp/pip-install-tfqvon7y/POT/setup.py'"'"'; file='"'"'/private/tmp/pip-install-tfqvon7y/POT/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/tmp/pip-wheel-0mnp0bwh --python-tag cp37
cwd: /private/tmp/pip-install-tfqvon7y/POT/
Complete output (49 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.7
creating build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/unbalanced.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/bregman.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/plot.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/stochastic.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/datasets.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/init.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/dr.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/utils.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/smooth.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/gromov.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/optim.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/da.py -> build/lib.macosx-10.7-x86_64-3.7/ot
creating build/lib.macosx-10.7-x86_64-3.7/ot/gpu
copying ot/gpu/bregman.py -> build/lib.macosx-10.7-x86_64-3.7/ot/gpu
copying ot/gpu/init.py -> build/lib.macosx-10.7-x86_64-3.7/ot/gpu
copying ot/gpu/utils.py -> build/lib.macosx-10.7-x86_64-3.7/ot/gpu
copying ot/gpu/da.py -> build/lib.macosx-10.7-x86_64-3.7/ot/gpu
creating build/lib.macosx-10.7-x86_64-3.7/ot/lp
copying ot/lp/init.py -> build/lib.macosx-10.7-x86_64-3.7/ot/lp
copying ot/lp/cvx.py -> build/lib.macosx-10.7-x86_64-3.7/ot/lp
creating build/lib.macosx-10.7-x86_64-3.7/ot/externals
copying ot/externals/funcsigs.py -> build/lib.macosx-10.7-x86_64-3.7/ot/externals
copying ot/externals/init.py -> build/lib.macosx-10.7-x86_64-3.7/ot/externals
running build_ext
building 'ot.lp.emd_wrap' extension
creating build/temp.macosx-10.7-x86_64-3.7
creating build/temp.macosx-10.7-x86_64-3.7/ot
creating build/temp.macosx-10.7-x86_64-3.7/ot/lp
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/chenlinwei/anaconda3/envs/DL3.7/include -arch x86_64 -I/Users/chenlinwei/anaconda3/envs/DL3.7/include -arch x86_64 -Iot/lp -I/Users/chenlinwei/anaconda3/envs/DL3.7/lib/python3.7/site-packages/numpy/core/include -I/private/tmp/pip-install-tfqvon7y/POT/ot/lp -I/Users/chenlinwei/anaconda3/envs/DL3.7/include/python3.7m -c ot/lp/emd_wrap.cpp -o build/temp.macosx-10.7-x86_64-3.7/ot/lp/emd_wrap.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 ot/lp/emd_wrap.cpp:470:
In file included from /Users/chenlinwei/anaconda3/envs/DL3.7/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/chenlinwei/anaconda3/envs/DL3.7/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/chenlinwei/anaconda3/envs/DL3.7/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/Users/chenlinwei/anaconda3/envs/DL3.7/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 "
^
In file included from ot/lp/emd_wrap.cpp:473:
ot/lp/EMD.h:19:10: fatal error: 'iostream' file not found
#include
^~~~~~~~~~
2 warnings and 1 error generated.
error: command 'gcc' failed with exit status 1

ERROR: Failed building wheel for POT
Running setup.py clean for POT
Failed to build POT
Installing collected packages: POT
Running setup.py install for POT ... error
ERROR: Command errored out with exit status 1:
command: /Users/chenlinwei/anaconda3/envs/DL3.7/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/tmp/pip-install-tfqvon7y/POT/setup.py'"'"'; file='"'"'/private/tmp/pip-install-tfqvon7y/POT/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/tmp/pip-record-ppjb9tmf/install-record.txt --single-version-externally-managed --compile
cwd: /private/tmp/pip-install-tfqvon7y/POT/
Complete output (49 lines):
running install
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.7
creating build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/unbalanced.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/bregman.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/plot.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/stochastic.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/datasets.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/init.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/dr.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/utils.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/smooth.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/gromov.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/optim.py -> build/lib.macosx-10.7-x86_64-3.7/ot
copying ot/da.py -> build/lib.macosx-10.7-x86_64-3.7/ot
creating build/lib.macosx-10.7-x86_64-3.7/ot/gpu
copying ot/gpu/bregman.py -> build/lib.macosx-10.7-x86_64-3.7/ot/gpu
copying ot/gpu/init.py -> build/lib.macosx-10.7-x86_64-3.7/ot/gpu
copying ot/gpu/utils.py -> build/lib.macosx-10.7-x86_64-3.7/ot/gpu
copying ot/gpu/da.py -> build/lib.macosx-10.7-x86_64-3.7/ot/gpu
creating build/lib.macosx-10.7-x86_64-3.7/ot/lp
copying ot/lp/init.py -> build/lib.macosx-10.7-x86_64-3.7/ot/lp
copying ot/lp/cvx.py -> build/lib.macosx-10.7-x86_64-3.7/ot/lp
creating build/lib.macosx-10.7-x86_64-3.7/ot/externals
copying ot/externals/funcsigs.py -> build/lib.macosx-10.7-x86_64-3.7/ot/externals
copying ot/externals/init.py -> build/lib.macosx-10.7-x86_64-3.7/ot/externals
running build_ext
building 'ot.lp.emd_wrap' extension
creating build/temp.macosx-10.7-x86_64-3.7
creating build/temp.macosx-10.7-x86_64-3.7/ot
creating build/temp.macosx-10.7-x86_64-3.7/ot/lp
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/chenlinwei/anaconda3/envs/DL3.7/include -arch x86_64 -I/Users/chenlinwei/anaconda3/envs/DL3.7/include -arch x86_64 -Iot/lp -I/Users/chenlinwei/anaconda3/envs/DL3.7/lib/python3.7/site-packages/numpy/core/include -I/private/tmp/pip-install-tfqvon7y/POT/ot/lp -I/Users/chenlinwei/anaconda3/envs/DL3.7/include/python3.7m -c ot/lp/emd_wrap.cpp -o build/temp.macosx-10.7-x86_64-3.7/ot/lp/emd_wrap.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 ot/lp/emd_wrap.cpp:470:
In file included from /Users/chenlinwei/anaconda3/envs/DL3.7/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/chenlinwei/anaconda3/envs/DL3.7/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/chenlinwei/anaconda3/envs/DL3.7/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/Users/chenlinwei/anaconda3/envs/DL3.7/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 "
^
In file included from ot/lp/emd_wrap.cpp:473:
ot/lp/EMD.h:19:10: fatal error: 'iostream' file not found
#include
^~~~~~~~~~
2 warnings and 1 error generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /Users/chenlinwei/anaconda3/envs/DL3.7/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/tmp/pip-install-tfqvon7y/POT/setup.py'"'"'; file='"'"'/private/tmp/pip-install-tfqvon7y/POT/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/tmp/pip-record-ppjb9tmf/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.

[rflamary]

Hello,

Note that the preferred installation on macosx is by using anaconda and the forge that has been compiled and tested.

But if you want to install it on macosx you might need an additional parameter as described in #113. To do that you just need to download the source and edit the setup.py.

I don't have a mac so this kind of error can be caught a bit late. @ncourty could you have a look at it (also bug #113 )?

[rflamary]

This should be working now since #130